COST_INDEPTH Kick Off Meeting

Transcription

1 COST_INDEPTH Kick Off Meeting Date and Time Title Authors Abstract Clermont Ferrand March 12th-14th 2018

2 Welcome to Clermont-Ferrand On behalf of the COST-Action CA16212 Impact of Nuclear Domains in Gene Expression and Plant Traits (INDEPTH), we are very pleased to welcome all participants to Clermont-Ferrand in the Auvergne Region. Clermont-Ferrand is famous for its very special black stone architecture in the old city centre, which is best embodied by its gothic cathedral but also because it is located in an exceptional natural environment surrounded by volcanoes. Clermont Auvergne University and the Genetics, Reproduction and Development laboratory (GReD) are very pleased to coordinate the INDEPTH challenge. INDEPTH brings together research communities to foster integrative plant research aiming to decipher the inter-related regulatory processes interpreting the genome in model and crop species with particular emphasis on the role of nuclear domains in gene expression control. We hope that you will enjoy your stay and wish you an interesting and motivating kick-off meeting. The organisers: Aline, Claire and Christophe 2 3

3 Meeting Information For all meeting information please contact: Claire Pelissier: The meeting will take place at: Maison Internationale Universitaire, 9 Rue Kessler, Clermont-Ferrand (Phone: ) Information about GReD The GReD is a Research Unit in Clermont-Ferrand, in the Auvergne Rhône-Alpes region of France. Created in 2008, the GReD is supported by the University Clermont Auvergne (UCA), the Centre National de la Recherche (CNRS) and the Institut National de la Santé Et de la Recherche Médicale (INSERM). The GReD is situated in the Centre de Recherche Bio-Clinique (CRBC) on the campus of the Faculty of Medicine and involves around 150 researchers, teachers, students, postdocs, engineers and technicians organized in 14 research teams ( ). COST is an EU-funded programme that enables researchers to set up their interdisciplinary research networks in Europe and beyond. We provide funds for organising conferences, meetings, training schools, short scientific exchanges or other networking activities in a wide range of scientific topics. By creating open spaces where people and ideas can grow, we unlock the full potential of science. Our research addresses (1) Genome dynamics and epigenetic control, (2) Reproduction and development in health and disease and (3) Endocrinology, signalling and cancer. These three research axes combine molecular and cellular biology, imaging and genetics and bridge the use of multiple model species including vertebrates, insects and plants to clinical applications to strengthen the continuum between basic and clinical research. Axis 1 of the GReD related to the INDEPTH COST- Action aims at understanding the genetic and epigenetic programs required for development and reproduction, and how deregulation of these complex processes can result in disease. 4 5

4 Detailed Schedule Monday March 12 th :00-12:00: Meeting for members of INDEPTH Management Committee 11:00-12:00: Arrival/Registration and Poster setup for general delegates 12:00-12:30: Welcome to the Université Clermont Auvergne (UCA) Pierre-Charles Romond (UCA Vice-president), Chantal Vaury (Head of GReD laboratory). 12:30-13:30: Lunch Official introduction to the INDEPTH COST Action: Chair Christophe Tatout (Université Clermont Auvergne) Vice-Chair Célia Baroux (University of Zürich) Science Officer Ioanna Stavridou (COST programme) 13: : Opening Keynote: Daniel Schubert (Freie Universität Berlin): Chromatin Regulation At The Nuclear Envelope In Arabidopsis 14: WG1:Quantitative imaging and analysis of the plant nucleus in 3D : Introduction: Katja Graumann (Oxford Brookes) and Dimiter Prodanov (University of Leuven) : Paul Fransz (University of Amsterdam): 3D Nuclear Organisation In Arabidopsis thaliana : Susan Duncan (Earlham Institute): icefish: a method to interrogate regulation and infer nuclear chromosome positioning in hexaploidy bread wheat : Tao Dumur (Gregor Mendel Institute): Dynamic nuclear architecture in root cells during long heat stress : Célia Baroux (University of Zürich): Role of linker histones on chromatin organisation in Arabidopsis from the nuclear level to the nanoscale : Coffee Break : Dimiter Prodanov (University of Leuven): Segmentation and classification of cells in microscopic image : Zikrija Avdagic (University of Sarajevo): Framework for processing 3D+time microscopy images using fusion of articial intelligence methods and statistics : Zofia Parteka (University of Warsaw): 3D chromatin modelling from imaging data : Christophe Tatout (Université Clermont Auvergne): Linking nuclear structure and function through 3D-imaging 17:35-19:00: Parallel WG meetings (WG1-4) 19: : Posters with drinks and hot buffet 6 7

5 Detailed Schedule Tuesday March 13 th : : Keynote Plenary: David Evans (Oxford Brookes): Exploring the Proteins of the Plant Nuclear Envelope :00: WG4: Storage, Data management and integrative analysis 9:15-9:25: Introduction by WG4 leaders. Björn Grüning (University of Freiburg) and Stefan Grob (University of Zürich) 9:25-9:45: Giorgio Papadopoulos (University of Montpellier): Integrative analysis of gene expression regulatory mechanisms. 9: : Björn Gruening (University of Freiburg): The GALAXY platform for accessible, reproducible and collaborative big-data analyses 10:05-10:20: Rémy Malgouyres (Université Clermont Auvergne): WRAPSCIENCEJ: an integrative multipurpose platform for data analysis on a distributed infrastructure. 10:20-10:35: Michał Kadlof (University of Warsaw) 3D genome modelling methods that combine genomic and epigenomic data Tuesday March 13 th : WG3: Structure of nuclear domains and the functional output for plant traits. 11:05-11:15: Introduction by WG3 leaders: Ales Pecinka (Institute of Experimental Botany) and Monica Pradillo (University Complutense of Madrid) :35: Christian Chevalier (Université de Bordeaux): DNA-Dependent Fruit Growth in Tomato: Nuclear Ploidy Levels and Gene Expression 11:35-11:50: Stefanie Rosa (Swedish University of Agricultural Science): Studying transcription coordination at the single locus level using single molecule RNA FISH 11: : Marta Koblowska (University of Warsaw): Time-series experiment reveals new epigenetic signature and a gene regulatory network involved in early response to salinity stress in Arabidopsis T87 cells :20: Nadia Fernández (University Complutense of Madrid) The nucleoporins suppressor of Auxin Resistance (SAR1) and SAR3, and chromatin: a complex affaire during meiosis 12:20-13:30:Lunch with posters : Coffee Break 8 9

6 Detailed Schedule Tuesday March 13 th :50: Isabelle Colas (James Hutton Institute): Modulation of Meiotic Recombination in Barley 13:50-14:05: Danny Geelen (Ghent University): PROTEIN PHOSHATASE 2A protects sister chromatid cohesion in Arabidopsis male meiosis I by maintaining cohesin SYN1at centromeres 14: : Ales Pecinka (Institute of Experimental Botany): Plant chromatin organisation under ambient and stress conditions 14:20-14:35: Serena Varotto (University of Padova): Discovering the epigenetic memory of stress response in maize :00: Social event- Tour of Clermont-Ferrand 17: : Coffee Break 17:30-18:30: Introduction to WG5: Dissemination and Training: Geraint Parry (Cardiff University) Aline Probst (Université Clermont Auvergne) : Parallel Session: Core group Meeting and Poster session 19:30-20:30: Wine reception and buffet 20:30-22:00: Brainstorming, skills matching session and STSM discusssions Chair: David Evans. STSM grantees: Mariamawit Ashenafi (University of Zürich) and Gianluca Teano (IBENS Paris) Wednesday March 14 th : WG2: Transcriptional regulation through association of chromatin domains with nuclear compartments : Introduction by WG2 Leaders. Stefanie Rosa (Swedish University of Agricultural Science) and Sara Farrona (University of Galway) : Frederic Pontvianne (Université de Perpignan): Elucidating the role of the nucleolus in the global chromatin organization : Martina Dvorácková (CEITEC, Masaryk University): Replication and Transcription inside the Nucleolus : Rafal Archacki (University of Warsaw): Mechanisms of transcriptional regulation by Arabidopsis chromatin remodeler BRM : Szymon Swiezewski (University of Warsaw): Antisense Transcription and its role in seed dormancy regulation : Coffee Break 10 11

7 Detailed Schedule Wednesday March 14 th : Chang Liu (University of Tübingen): Plant Lamin-Like Proteins And Non-CG Dna Methylation Mediate Specific Chromatin Tethering At The Nuclear Periphery : Lauriane Simon (Swedish University of Agricultural Science): A Potential New H3K9me2 Methyltransferase Acting In the Endosperm : Fredy Barneche (IBENS Paris): A linker histone variant drives light-controlled heterochromatin rearrangements in Arabidopsis : Stefan Grob (University of Zürich): Transgene Silencing in 3D How a Chromosomal Knot Can Inactivate Foreign DNA Elements : Meeting Wrap up and Future Plans. Discus sion lead: Christophe Tatout : Lunch and Exit 12 13

8 13.30pm March 12th Keynote CHROMATIN REGULATION AT THE NUCLEAR ENVELOPE IN ARABIDOPSIS Daniel Schubert 1,3, Kalyanikrishna 1, Pawel Mikulski 1,2,3, Mareike Hohenstatt 3 1- Institute of Biology, Freie Universität Berlin, Germany 2- John Innes Centre, Norwich, UK 3- Institute for Genetics, Heinrich-Heine-University Düsseldorf, Germany dan.schubert@fu-berlin.de Three-dimensional structuring of chromatin contributes to gene activation and repression. Constitutive heterochromatin is anchored at the nuclear envelope and the nucleoli, but the positioning of facultative heterochromatin in the nuclear space is less clear. Polycomb-group (PcG) proteins promote facultative heterochromatin formation via tri-methylation of lysine 27 on histone H3 (H3K27me3) and epigenetically repress developmental and stress responsive genes. We have identified a novel chromatin protein family in Arabidopsis, PWWP INTERACTOR OF POLYCOMBS1 (PWO family) that interacts with PcG proteins and histone H3. Importantly, it recruits PcG proteins to the nuclear envelope, to speckle-like structures, in transient transformation assays. PWO1 also interacts with proteins of the nuclear lamina in Arabidopsis, including CROWDED NUCLEI 1 (CRWN1) and CRWN4 proteins. PWO1 and CRWN1 regulate nuclear size and control expression of a similar set of stress responsive genes. In addition, the PWO1 family is an important regulator of plant development, as PWO1 and PWO3 promote FLOWERING LOCUS C expression and loss of the three proteins results in severe developmental defects, including seedling lethality and shoot and root meristem arrest. The PWWP domain of PWO1 mediates interaction with H3 and loss of PWO1 results in reduced H3 occupancy at PcG target genes. We therefore postulate that the PWO1 family mediates the interaction of PcG proteins, histones and the nuclear lamina and may recruit PcG proteins to specific (stress responsive target genes at the nuclear envelope. Dittmer, T. A et al (2007). Plant Cell. 19(9): Hohenstatt, L.M et al (2018). PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 interacts with Polycomb- group proteins and histones and regulates Arabidopsis flowering and development. Plant Cell 30 (1), Mikulski P et al (2017). PWWP INTERACTOR OF POLYCOMBS (PWO1) links PcG-mediated gene repression to the nuclear lamina in Arabidopsis. biorxiv preprint, Sakamoto, Y., and Takagi, S. (2013). LITTLE NUCLEI 1 and 4 regulate nuclear morphology in Arabidopsis thaliana. Plant Cell Physiol. 54, Wang, H. et al (2013). Arabidopsis CROWDED NUCLEI (CRWN) proteins are required for nuclear size control and heterochromatin organization. BMC Plant Biol. 13,

9 3D NUCLEAR ORGANIZATION IN Arabidopsis thaliana P. Fransz, Till Bey, Penka Pavlova, Maria Koini and Hans de Jong Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands 14.30pm March 12th WG1 Most eukaryotes share the same principals of chromatin organization in relation to genome function and stability. Chromatin loops, which indicate close interaction of distant chromosomal regions, have been reported in several species. Also the specific distribution of euchromatin and heterochromatin domains is a distinct feature in the eukaryote nucleus. Despite similar principles of chromatin organization, there are several differences between plants and animals, but also among plant species. We investigate the organization of chromatin and chromosomal loci in the interphase nucleus in Arabidopsis using 2D and 3D approaches in combination with immunostaining and FISH detection. In this presentation the variation in nuclear organization under different conditions and in different cell types will be discussed. Snoek Fransz PF, (2017) Genetic Dissection of Morphometric Traits Reveals That Phytochrome B Affects Nucleus Size and Heterochromatin Organization in Arabidopsis thaliana. Genes, Genomes, Genetics 7, doi: /g Bourbousse C, Mestiri I, Zabulon G, Bourge M, Formiggini F, Koini MA, Brown SC, Fransz P, Bowler C, Barneche F. (2015) Light signaling controls nuclear architecture reorganization during seedling establishment. Proc Natl Acad Sci U S A. 112(21):E2836-E2844. Batzenschlager M, Lermontova I, Schubert V, Fuchs J, Berr A, Koini MA, Houlné G, Herzog E, Rutten T, Alioua A, Fransz P, Schmit AC, Chabouté ME. (2015) Arabidopsis MZT1 homologs GIP1 and GIP2 are essential for centromere architecture. Proc Natl Acad Sci U S A. 112(28): Van Zanten, F. Tessadori, A.J.M. Peeters and P. Fransz (2012) Shedding Light on Large-Scale Chromatin Reorganization in Arabidopsis thaliana. Molec. Plant 5,

10 icefish: A METHOD TO INTERROGATE TRANSCRIPTIONAL REGULATION AND INFER NUCLEAR CHROMOSOME POSITIONING IN HEXAPLOID BREAD WHEAT Susan Duncan and Anthony Hall Earlham Institute, Norwich Research Park, UK Address susan.duncan@earlham.ac.uk 14.50pm March 12th WG1 The common bread wheat genome is huge and highly complex. It consists of two copies of A, B and D subgenomes that are highly repetitive and share extensive regions of near-identical sequence. Fluorescent in situ hybridization chromosome painting has traditionally been used to visualize chromosomes in 3D, but this approach has been hampered in wheat as it relies on sequence variation for specific probe generation. Although it is known that wheat centromeres and telomeres are positioned at opposite poles of the nucleus in a Rabl conformation (Wegel and Shaw 2005), there are currently no effective microscopy methods to interrogate relative chromosome positions. Intron Chromosomal Expression RNA FISH (icefish) fluorescently labels nascent, intronic RNA (Levesque et al., 2013). This method has recently been used, together with single molecule RNA FISH (smfish), to provide novel insights into gene regulation and transcription dynamics in Arabidopsis (reviewed in Duncan and Rosa 2017). In addition to labelling active genes, icefish effectively marks gene positions within the nucleus as intronic RNA is typically turned over at the site of transcription. By taking advantage of differential subgenome expression patterns, multi-loci icefish could be used to infer relative A, B and D chromosome topologies. IceFISH is complementary to a range of other chromosome conformation assays (i.e. Hi-C, 5C, 4C, 3C) and could be a valuable tool for exploring the impact of nuclear organization on wheat gene expression. Duncan, S., Rosa, S. (2017) Gaining insight into plant gene regulation using smfish. Transcription. 1-5 Levesque, M.J., Raj, A. (2013). Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. Nat Methods.10: Wegel, E., and Shaw, P.J. (2005). Chromosome organization in wheat endosperm and embryo. Cytogenet Genome Res. 109:

11 15.05pm March 12th WG1 DYNAMIC NUCLEAR ARCHITECTURE IN ROOT CELLS DURING LONG HEAT STRESS Tao Dumur 1, Jasmin Bassler 1, Nina Daubel 1, Miloš Šrámek 1, Christian Göschl 1, Malgorzata Goiser 1, Aline V. Probst 2, Ortrun Mittelsten Scheid 1 1- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria 2- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont Ferrand, France Interphase nuclei of plant cells differ in shape and chromatin organization, and both features can vary following developmental cues, such as seed maturation 1 or flowering induction 2, or in response to abiotic factors, such as heat stress 3. Particularly, upon prolonged heat stress, Arabidopsis nuclei were shown to have decondensed chromocenters, concomitant with transcriptional reactivation of many genes, including silent repetitive elements. The changes in nuclear architecture were so far documented based on staining of fixed and isolated nuclei, not allowing to consider tissue context or the fate of the nuclei after the stress. We have now developed a live-imaging setup that allows monitoring nuclear architecture in living root cells over long periods and during stress application. We show that prolonged heat stress leads to a progressive and transient change from spindle-like towards spherical nuclear shapes, accompanied by heterochromatin decondensation. We are currently investigating the role of different histone chaperones and members of the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex in controlling nuclear shape and chromatin compaction in response to prolonged heat stress. 1. van Zanten, M., Koini, M. A., Geyer, R., Liu, Y., Brambilla, V., Bartels, D., et al. (2011). Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation. Proceedings of the National Academy of Sciences of the United States of America, 108 (50), Tessadori, F., Schulkes, R. K., Driel, R. V., & Fransz, P. (2007). Light-regulated large-scale reorganization of chromatin during the floral transition in Arabidopsis. The Plant Journal, 50 (5), Pecinka, A., Dinh, H. Q., Baubec, T., Rosa, M., Lettner, N., & Mittelsten Scheid, O. (2010). Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell, 22(9),

12 ROLE OF LINKER HISTONES ON CHROMATIN ORGANISATION IN ARABIDOPSIS FROM THE NUCLEAR LEVEL TO THE NANOSCALE Kinga Rutowicz 1#, Maciek Lirski 2#,Benoît Mermaz 1,3, Mariamawit Ashenafi 1, Fabrice Tonhyui 1, Andrzej Jerzmanowski 2 and Célia Baroux 1 1-Department of Plant and Microbial Biology, University of Zürich, Switzerland 2-Institute of Plant Molecular Biology, University of Warsaw, Poland 3-Department of Life Sciences, Imperial College London, United-Kingdom cbaroux@botinst.uzh.ch 15.20pm March 12th WG1 H1 linker histones are evolutionary conserved chromatin proteins sharing a structural role in chromosome compaction and chromatin fiber organization throughout eukaryotes. H1 s also have a function in gene regulation by influencing the DNA methylation landscape in both plants and animals (Fan et al, 2005; Wierzbicki et al 2005, Zemach et al, 2013). Arabidopsis possess three canonical H1 variants, one of which, H1.3, acting as a facilitator of cellular reprogramming in abiotic stress responses (Rutowicz et al 2015). H1.1 and H1.2 are somatic variants robustly expressed throughout development. These variants exhibit, however, a peculiar dynamics at the somatic-toreproductive fate transition coinciding with large-scale chromatin reprogramming (She et al, 2013). Arabidopsis is generally resilient to the loss of H1 function with phenotypes ranging from abnormal vegetative development to mild flowering time alteration depending on the genetic perturbation (RNAi or triple T-DNA insertions). We report here on the specific influence of H1 s on chromatin organization in Arabidopsis. Using a combination of chromatin accessibility assays, cytogenetic approaches, high- and super- resolution microscopy, transmission electron microscopy and customized image processing we characterized distinct roles for H1 on heterochromatin and euchromatin at the microscopic, nanoscopic and nucleosomal levels. Fan, Y et al (2005). Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell 123(7): Rutowicz, K et al (2015). A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis. Plant Physiol 169(3): She, W et al (2013). Chromatin reprogramming during the somatic-to-reproductive cell fate transition in plants. Development 140(19): Wierzbicki, A. T. and A. Jerzmanowski (2005). Suppression of histone H1 genes in Arabidopsis results in heritable developmental defects and stochastic changes in DNA methylation. Genetics 169(2): Zemach, A et al (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153(1):

13 SEGMENTATION AND CLASSIFICATION OF CELLS IN MICROSCOPIC IMAGES Dimiter Prodanov EHS, IMEC, Leuven, Belgium 16.30pm March 12th WG1 Modern microscopy allows for acquisition of images spanning in different spectral, spatial and temporal dimensions. Once acquired, these frequently huge images need to be condensed into few quantitative statements that can either support or falsify the initial research questions. This process of measurement and analysis nowadays cannot be performed without the use of specialized software toolboxes. These toolboxes make the backbone of bioimage informatics, a newly defined branch of bioinformatics. Image segmentation and object recognition are crucial applications in bioimaging informatics. While there are no generic solutions of these problems several classes of algorithms provide acceptable results to most of the applied problems. Common approaches range from intensity based to texture and geometry based. Selected applications of these approaches include segmentation of nuclei, cell bodies and tissue textures. The lecture will give overview of some of the most widely used techniques with emphasis on multiscale approaches and wavelets. Implementations of various techniques will be demonstrated using the popular image analysis platform ImageJ. Secondly, applications of machine learning techniques will also be demonstrated as specific toolbox implementations

14 FRAMEWORK FOR PROCESSING 3D+Time MICROSCOPY IMAGES USING FUSION OF ARTIFICIAL INTELLIGENCE METHODS AND STATISTICS Zikrija Avdagic, Samir Omanovic University of Sarajevo, Faculty of Electrical Engineering, Department for Computing and Informatics, Zmaja od Bosne bb, Sarjevo, Bosnia and Herzegovina 16.50pm March 12th WG1 Despite recent breakthroughs in 3D microscopy imaging, building an approach that will achieve high precision, reliability and generalization in 3D nucleus domains imaging remains a difficult task. We present here Framework integrating all steps from image acquisition, advanced image analysis, 3D volume pattern recognition, behavior prediction and visualization. Mathematical models and software for 3D image segmentation, recognition and 3D+t prediction of the predetermined nucleus domain volume change would be developed using fusion of artificial methods and statistics. In the process of sample preparation, in accordance with the protocols, 3D images of plant samples are colected s days forming time-series of daily sets S={S1,S2,...,Ss} in which each daily set Si includes l samples, Si={si,1,si,2,...,si,l} for i=1,2,...,s. Each day is generated one set of conditions Xi=(xi,1,xi,2,...,xi,n), and for s days have time-series of daily conditions X={X1,X2,...,Xs}. In the segmentation process, several methods (clustering, machine and deep learning, genetic algorithms, ) are used in the majority voting system. Daily result are processed and based on statistics, one representative sample is selected forming time series R={R1,R2,,Rs}. 3D image (voxels representation) is used to generate descriptors. Elements detected on 3D image can be modelled mathematically to get 3D vector model to enable easer visualisation and usage of vector mathematics. Each day is generated one set of model characteristics Yi=(yi,1,yi,2,...,yi,m), and we have models time-series Y={Y1,Y2...,Ys} for s days. Based on segment descriptors D={D1,D2,...,Ds} and manually assigned labels L={L1,L2,...,Ls} is created automatic annotation of segments. Based on X and Y are created predictors: Y(s+1)=f(Y(s),...,Y(s-d)), Y(s+1)=f(X(s),...,X(s-d)), and X(s+1)=f(Y(s),...,Y(s-d)). Faure, E. et al. (2015). A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage. NATURE COMMUNICATIONS, 7:8674, DOI: / ncomms9674. Long, F et al (2012). Visualization and Analysis of 3D Microscopic Images. PLOS Computational Biology, Merchant, F. A (2008). Three-Dimensional Imaging. Microscope Image Processing, Pages ,

15 3D CHROMATIN MODELLING FROM IMAGING DATA Zofia Parteka 1,2, Michał Kadlof 1,3, Przemysław Szałaj 1,4,5, Jufen Zhu 6, Yijun Ruan 6, Dariusz Plewczynski 6 1- Centre of New Technologies, University of Warsaw, Poland 2- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland 3- Faculty of Physics, University of Warsaw, Poland 4- Medical University of Bialystok, Center for Bioinformatics and Data Analysis Poland 5- I-BioStat, Hasselt University, Belgium 6- Jackson Laboratory for Genomic Medicine, CT, USA z.parteka@cent.uw.edu.pl 17.05pm March 12th WG1 The three-dimensional structure of chromatin is of fundamental importance for gene regulation and cellular function. I t determines genome compaction and activity in the nucleus. Chromatin fibers form many different loops and a variety of dynamic conformations to achieve structural high packing density. However, the spatial organisation of chromatin fiber have been difficult to observe using conventional microscopy. Recent developments in microscopy allow us to study genome conformation and chromatin contacts using not only high-throughput genomic data (Hi-C, ChIA-PET) but also chromatin imaging data at different resolution. We present multiple chromatin modeling methods developed in our laboratory. Presently our main focus is on building 3D chromatin models from variety of available experimental data. In addition to genome mapping data we are working on using different microscopy techniques in our algorithms. Our aim is to process images from confocal microscopy, super-resolution microscopy and electron microscopy to obtain markers for chromatin density and precise positions of chromatin fiber. We developed several algorithms to visualise positions, shapes and the volumes of chromosomal territories in the nucleus as well as procedures to build more precise chromatin structures at different scales. Our goal is to compute image driven models that can be compared to genomic data driven models. Szalaj, P., Tang, Z., Michalski, P.J., Pietal, M., Luo, O., Sadowski, M., Li, X., Radew, K., Ruan, Y., and Plewczynski, D. (2016). An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. Genome Res. 26, Szalaj, P., Michalski, P.J., Wroblewski, P., Tang, Z., Kadlof, M., Mazzocco, G., Ruan, Y. and Plewczynski, D. (2016) 3D-GNOME: an integrated web service for structural modeling of the 3D genome. Nucleic Acids Res. 44, W288 W293 Tang, Z., Luo, O.J., Li, X., Zheng, M., Zhu, J.J., Szalaj, P., et al. (2015) CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell. 163,

16 LINKING NUCLEAR STRUCTURE AND FUNCTION THROUGH 3D- IMAGING Christophe Tatout 1, Rémy Malgouyres 2, Aline V. Probst 1 and Sophie Desset 1 1- UMR CNRS GReD, Clermont Université, INSERM U 931, 24 avenue des Landais, Aubière, France 2- UCA, ISIMA, Campus des Cézeaux, 1 rue de la Chebarde Aubière, France Christophe.tatout@uca.fr 17.20pm March 12th WG1 The nucleus is a compartmentalized organelle containing distinct chromosomal domains and nuclear bodies. To link nuclear structure and function, we have developed NucleusJ (Poulet et al., 2015), a 3D imaging tools to quantify nuclear morphology as well as positioning and organization of chromatin domains. The initial version of NucleusJ is a simple and user-friendly ImageJ plugin. From confocal images, the programme applies a modified Otsu thresholding method to segment the nuclear space and a 3D watershed algorithm to delimit chromatin domains by partitioning the nucleus. 15 parameters are computed including shape and size of nuclei as well as intra- nuclear objects such as chromatin domains and their position in respect to the nuclear periphery. The current NucleusJ version involves manual intervention to delimit a bounding volume including each considered nucleus. To overcome this limitation and automatically capture large numbers of nuclei at various depths in the sample, we have developed an automatic detection of the nucleus (autocrop). Spatial positions of the cropped nuclei are then recorded in order to estimate distance maps as a new estimator of spatial distribution of the nuclei in a whole tissue context. Finally, the software is now implemented into the new multi-purpose platform called WrapScienceJ (see abstract from R. Malgouyres) to become independent from ImageJ and to be connected with other softwares such as OMERO for image storage. These new functionalities will be illustrated through our recent efforts to characterize a range of mutants of nuclear envelope and nuclear envelope-associated proteins (Desset et al., 2018; Poulet et al., 2017). Desset, S., Poulet, A., and Tatout, C. (2018). Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ. Methods Mol. Biol. 1675, Poulet, A., Arganda-Carreras, I., Legland, D., Probst, A.V., Andrey, P., and Tatout, C. (2015). NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. Bioinformatics 31, Poulet, A., Duc, C., Voisin, M., Desset, S., Tutois, S., Vanrobays, E., Benoit, M., Evans, D.E., Probst, A.V., and Tatout, C. (2017). The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants. J Cell Sci 130,

17 EXPLORING THE PROTEINS OF THE PLANT NUCLEAR ENVELOPE David E Evans and Katja Graumann Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington Campus, Oxford, OX3 0BP, UK. deevans@brookes.ac.uk 08.30pm March 13th Keynote The nuclear envelope is known as a multi-functional structure of great importance in the eukaryotic cell. Different approaches to the study of the structure, function and regulation of the nucleus have revealed a combination of properties of the envelope, which enable functions as diverse as signal transduction, positioning the nucleus and structures in the nucleus, regulating gene expression, controlling transport between the nucleoplasm and cytoplasm and in achieving effective mitosis and meiosis. This talk will build from our understanding of one of the most highly conserved nuclear envelope proteins- the SUN domain family- to consider the discovery and role of other members of the Linked of Nucleoskeleton and Cytoskeleton (LINC) complex in plants. The role of the LINC complex as the basis for complex cytosketal and nucleoskeletal interactions will then be considered as a central pillar of the work of the INDEPTH COST action to characterise the way in which plant nuclear architecture, chromatin organization and gene expression are connected and modified in response to internal and external signals

18 INTEGRATIVE ANALYSIS OF GENE EXPRESSION REGULATORY MECHANISMS Papadopoulos GL, Karkoulia E, Pancaldi V and Cavalli G Institute of Human Genetics, 141 rue de la Cardonille, Montpellier - FRANCE giorgio.papadopoulos@igh.cnrs.fr 09.25pm March 13th WG4 Consolidation of NGS technologies provided the means for a highly accurate characterization of the epigenetic, transcriptomic and, more recently, chromosome organization states of different cell populations. Biological interpretation of these data allows and demands for the development of systemic approaches able to integrate these comprehensive sets and allow for the identification of underlying patterns and potential regulatory events. Here we propose a computational analysis pipeline that relies on the combination of supervised (RandomForest regression) and unsupervised (hierarchical clustering) machine learning algorithms to produce highly structured gene wide distribution patterns of chromatin features (Papadopoulos et al, 2013). As a result, we identify a series of distinct subsets of genes, characterized by the combinatorial similarity of their epigenetic and transcriptional states in different cell populations, greatly simplifying biological interpretation of the primary data. This pipeline was successfully applied in a range of biological processes (e.g. erythroid lineage differentiation and commitment), settings (e.g. restricting the analysis on different subsets of genes, modeling differential gene expression or differential chromatin levels) and different combinations of NGS datasets (e.g. histone modifications, TF occupancy and DNase hypersensitivity), thus suggesting its general applicability in the analysis and interpretation of complex genomic data. Finally, we employed a network-based approach to integrate HiC based chromosome conformation information into the model (Hsu et al., 2017). More specifically, we used chromatin assortativity to integrate the epigenetic landscape of a specific cell type with its chromatin interaction network and thus investigate which proteins or chromatin marks mediate genomic contacts (Pancaldi et al, 2016). Papadopoulos, G et al (2013). GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. Nucleic Acids Research, 41(9), pp Hsu, S et al (2017). The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Molecular Cell, 66(1), pp e7. Pancaldi, V et al (2016). Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity. Genome Biology, 17(1)

19 THE GALAXY PLATFORM FOR ACCESSIBLE, REPRODUCIBLE AND COLLABORATIVE BIG-DATA ANALYSES Bjoern Grüning and the Galaxy community Galaxy team Freiburg Albert-Ludwigs-Universität Freiburg Georges-Köhler-Allee Freiburg 09.45pm March 13th WG4 High-throughput data production technologies are responsible for disruptive changes in modern biomedical research. Interpretation of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. The Galaxy project tries to solve this by providing a framework for accessible, reproducible and collaborative data analysis to ensure the researcher participation on their own data. Galaxy ( european public server: eu) is a web- based scientific analysis platform used by thousand of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics, and imaging. In this talk we will present the fundamentals of Galaxy and the core community projects. We will introduce the Galaxy training network and real-world cases on how researchers use Galaxy to perform OMICS analysis today. Special emphasis will be given to the Galaxy Genome Annotation project and the interaction of Galaxy with other community projects like Tripal, Apollo, JBrowse, UCSC and Circos

20 WRAPSCIENCEJ: AN INTEGRATIVE MULTIPURPOSE PLATFORM FOR DATA ANALYSIS ON A DISTRIBUTED INFRASTRUCTURE Rémy Malgouyres UCA, ISIMA, Campus des Cézeaux, 1 rue de la Chebarde Aubière, France remy@malgouyres.org 10.05pm March 13th WG4 We present a new interoperability platform implemented in Java, called WrapScienceJ designed for integrative data analysis on a distributed infrastructure. It makes intensive use of the Bridge Design Pattern to allow third party Software or Hardware Providers to plug in softwares of their own, either to attract new customers or to ensure compatibility with their own products. The platform uses the contemporary concept of Metaprogramming to project Software Services on different existing platforms or interfaces (e.g. Application Programming Interfaces or Graphical User Interfaces). A Proof of Concept (*) will be presented which exposes key functionalities in Image Processing, basic Image Display, and an Open Source implementation based on a Wrapper of the ImageJ API. This already allows: - Very High Standards for Programming Interface Specifications aiming at Highly Reproducible Algorithms; - Higher Level Programming using Unit Tested Functionalities; - Metadata Modeling and automated retrieval of Metadata and automatic dialog generation; - Automated Generation of ready to deploy ImageJ Plugins; - Bridge Design allowing for new Implementation Policies, either for Display, Graphical User Interface Framework, or Image Processing Core Implementation; - Examples of Modules built on top of the Platform providing higher level image processing features. Future versions of the platform aim at transparent combinations of different modalities and data using higher level java programming. The current computations may be performed by another program in a different language, following the Bridge Design Pattern principle and using various ways to enable compatibility (e.g. JNI or Web Services), in a global Service Oriented Architecture (SOA). (*) A Source Code Release ought to be available by the time of the Meeting

21 3D GENOME MODELLING METHODS THAT COMBINE GENOMIC AND EPIGENOMIC DATA Michał Kadlof 1,2, Zofia Parteka 1, Przemysław Szałaj 1,3,4, Michał Łazniewski 1, Michał Sadowski 1,2, Zhonghui Tang 5, Yijun Ruan 5, Dariusz Plewczynski 1, 1- Centre of New Technologies, University of Warsaw, Poland 2- Faculty of Physics, University of Warsaw, Poland 3- Medical University of Bialystok, Center for Bioinformatics and Data Analysis, Poland 4. I-BioStat, Hasselt University, Belgium 5- Jackson Laboratory for Genomic Medicine, CT, USA 10.20pm March 13th WG4 We are currently observing an extremely intense development of highthroughput methods for the identification of contacts in the whole genome. Methods such as Hi-C or ChIA-PET (Chromatin Interaction Analysis by Paired-End Tag Sequencing) have made it possible to obtain more and more precise contact maps in scales from single loops and TAD (Topologically Associating Domains) to whole chromosomes. The increasing availability of high-quality data for the first time has enabled the development of 3D modeling methods on such scale. In combination with epigenomic data for the first time we obtain the possibility of data integration from two independent and complementary sources. This data can be used in two ways: to obtain more realistic models of genomics domains as well as for the purpose of verification of modeling methods. In this work, we present a wide spectrum of various approaches to modeling issues. In our laboratory, we develop methods based on statistical approach (Multidimensional Scaling), probabilistic (MMC Multiscale Monte Carlo), and biophysical (SM and MD Spring Model and Molecular Dynamics) methods. Each of these methods provides insight into a separate aspect of the genome structure of the organism under study. We also explore novel approach image-driven modeling which employs imaging data into already established methods. Tang, Z., Luo, O.J., Li, X., Zheng, M., Zhu, J.J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., et al. (2015). CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell Szałaj, P., Tang, Z., Michalski, P., Pietal, M.J., Luo, O.J., Sadowski, M., Li, X., Radew, K., Ruan, Y., and Plewczynski, D. (2016). An integrated 3-dimensional genome modeling engine for data-driven simulation of spatial genome organization. Genome Res. gr Szalaj, P., Michalski, P.J., Wróblewski, P., Tang, Z., Kadlof, M., Mazzocco, G., Ruan, Y., and Plewczynski, D. (2016). 3D-GNOME: an integrated web service for structural modeling of the 3D genome. Nucleic Acids Res. 44, gkw

22 DNA-DEPENDENT FRUIT GROWTH IN TOMATO: NUCLEAR PLODY LEVELS AND GENE EXPRESSION Christian Chevalier UMR1332 Biologie du Fruit et Pathologie, INRA Nouvelle-Aquitaine-Bordeaux, 71 avenue Bourlaux, CS20032, Villenave d Ornon cedex, France christian.chevalier@inra.fr 11.15pm March 13th WG3 As part of normal development most eukaryotic organisms ranging from insects to mammals and plants display variations in nuclear ploidy levels resulting from somatic endopolyploidy (Lee et al., 2009). Endoreduplication is the major source of endopolyploidy in higher plants. Endoreduplication is a remarkable characteristic of the fleshy pericarp tissue of developing tomato fruits, where it establishes a highly integrated cellular system that acts as a morphogenetic factor supporting cell growth (Bourdon et al., 2012; Chevalier et al., 2014). However, the functional significance of endoreduplication is not fully understood. Endoreduplication has long been described as a mean to increase metabolic activity due to a global increase in transcription However, it has never been fully demonstrated, and the issue of gene-specific ploidy-regulated transcription remains opened. The influence of endoreduplication on transcription in tomato fruit was thus investigated using various approaches, and in particular a RNA-Seq experiment based on total nuclear RNA extracted from purified populations of flow cytometry-sorted nuclei (Pirrello et al., 2018). From ploidy- specific expression profiles we found that the activity of cells inside the pericarp is related both to the ploidy level and their tissue location. Bourdon, M et al (2012). Evidence for karyoplasmic homeostasis during endoreduplication and a ploidy-dependent increase in gene transcription during tomato fruit growth. Development 139, Chevalier, C et al (2013). Endoreduplication and fruit growth in tomato: evidences in favor of the karyoplasmic ratio theory. J. Exp. Bot. 65, Lee, HO et al (2009). Endoreplication: Polyploidy with purpose. Genes Dev 23, Pirrello, J et al (2018). Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation. Plant J. 93,

23 MAPK-TRIGGERED CHROMATIN REPROGRAMMING BY HISTONE DEACETYLASE IN PLANT INNATE IMMUNITY David Latrasse, Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras, Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, Juan S. Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, Baptise Genot, T on Bisseling, Moussa Benhamed, Heribert Hirt Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France david.latrasse@u-psud.fr 11.35pm March 13th WG3 Microbial-associated molecular patterns (MAMPs) activate several MAP Kinases, which are major regulators of the innate immune response in Arabidopsis that induce large-scale changes in gene expression. Here, we determine whether microbialassociated molecular pattern-triggered gene expression involves modifications at the chromatin level. Our results show that histone acetylation and deacetylation are major regulators of MAMP-triggered gene expression and implicate the histone deacetylase HD2B in the reprogramming of defense gene expression and innate immunity. HD2B interacts directly with and is phosphorylated by MPK3, thereby regulating the intra-nuclear compartmentalization of HD2B. By studying a number of gene loci that undergo MAMPdependent activation or repression, our data reveal a mechanistic model for how protein kinase signaling directly impacts chromatin reprogramming in plant defense. Latrasse D, Jégu T, Li H, de Zelicourt A, Raynaud C, Legras S, Gust A, Samajova O, Veluchamy A, Rayapuram N, Ramirez-Prado J, Kulikova O, Colcombet J, Bigeard J, Genot B, Bisseling T, Benhamed M, Hirt H. (2017). MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity. Genome Biology. Jul 6;18(1):131. doi: /s LATE NOTICE: TALK REPLACED BY STEFANIE ROSA: SEE POSTER ABSTRACT WG1.3 PAGE

24 TIME-SERIES EXPERIMENT REVEALS NEW EPIGENETIC SIGNATURE AND A GENE REGULATORY NETWORK INVOLVED IN EARLY RESPONSE TO SALINITY STRESS IN ARABIDOPSIS T87 CELLS. Anna Fogtman 2, Aleksandra Kwiatkowska 1, Norbert Dojer 3, Roksana Iwanicka-Nowicka 1,2, Adrianna Pacek 1, Maciej Kotlinski 1, Jerzy Tiuryn 3, Andrzej Jerzmanowski 1,2 Marta Koblowska 1,2 1- Laboratory of Systems Biology, Faculty of Biology University of Warsaw Warsaw Poland 2. Institute of Biochemistry and Biophysics Polish Academy of Sciences WarsawPoland 3. Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland. marta@ibb.waw.pl 11.50pm March 13th WG3 One of the major abiotic constrains affecting plant growth is soil salinity. Despite many years of studying the molecular basis of plant response to high salinity we still have gaps in our understanding of complex mechanisms underlying plant tolerance to salinity. To advance our knowledge of the early stages in plant cell response to salinity, we carried out a time- series experiments during first 100 minutes of high-salt stress. As the most suitable model for performed studies we chosen Arabidopsis T87 cell line offering a relative cellular homogeneity comparing to a mixture of cells building the whole seedling or their organs. Our previous results describing nucleosomal response to high salinity, cold and ABA (Sokol et al., 2007) showed that Arabidopsis T87 cell line is a very convenient model to analyze stress response at the cellular level. To establish if frequent passages had an impact on T87 cells genome, we characterized a genetic variation in T87 cells. Additionally to our previous data demonstrating that phosphorylation of histone H3 (H3S10ph) is a nucleosomal marker of cells standard behavior under stress (Sokol et al., 2007), we also showed a novel histone modification H4K16ac to be a valid epigenetic signature of plant stress response. Transcription profiling of T87 cells led to identification of previously unrecognized genes strongly activated during first minutes of salinity stress. Time-series transcriptome analysis during salinity stress followed by Bayesian network modelling recognized a set of hub genes directing the early response of plant cells to salinity stress. Sokol, A., Kwiatkowska, A., Jerzmanowski, A., and Prymakowska-Bosak, M. (2007). Up-regulation of stress-inducible genes in tobacco and Arabidopsis cells in response to abiotic stresses and ABA treatment correlates with dynamic changes in histone H3 and H4 modifications. Planta 227,

25 THE NUCLEOPORINS SUPPRESSOR OF AUXIN RESISTANCE1 (SAR1) AND SAR3, AND CHROMATIN: A COMPLEX AFFAIR DURING MEIOSIS Nadia Fernández, Mónica Pradillo Department of Physiology, Genetics and Microbiology, Faculty of Biology, Universidad Complutense de Madrid, Spain nadfer01@ucm.es 12.05pm March 13th WG3 During the early stages of meiosis, telomeres anchor chromosomes to the inner nuclear envelope (NE) and cluster together into a bouquet configuration. This structure facilitates pairing of homologous chromosomes. Among the factors that are required to connect telomeres to the NE are SUN domain proteins. In a previous study, we determined that AtSUN1 and AtSUN2 play an active and integral role in Arabidopsis meiotic progression, since the absence of these proteins results in a delay in meiotic progression associated with defects in synapsis and recombination (Varas et al., 2015). We wondered if, in addition to the SUN proteins, other NE-associated proteins play a role during meiosis. In order to highlight a potential function of the components of the Nuclear Pore Complexes (NPCs) in meiosis we have analyzed lines defective for nucleoporins that belong to the structural subcomplex NUP , specifically AtNUP160 and AtNUP96, also called SUPPRESSOR OF AUXIN RESISTANCE1 and 3, respectively. The cytological characterization of pollen mother cells (PMCs) in sar mutants has revealed the presence of a percentage of meiocytes with altered chromatin condensation and chromosome fragmentation. These defects do not seem to be related with epigenetic modifications and appear in both first and second meiotic divisions. In addition, we have determined that sar mutants are hypersensitive to different DNA damage agents. This study reveals a possible relationship between NPCs, meiosis and DNA repair that has not been previously reported in plants. Varas, J., Graumann, K., Osman, K., Pradillo, M., Evans, D.E., Santos, J.L., and Armstrong, S.J. (2015). Absence of SUN1 and SUN2 proteins in Arabidopsis thaliana leads to a delay in meiotic progression and defects in synapsis and recombination. Plant J 81,

26 MODULATION OF MEIOTIC RECOMBINATION IN BARLEY Mikel Arrieta, Isabelle Colas, Robbie Waugh and Luke Ramsay Cell and Molecular Sciences Group, James Hutton Institute, Errol Road, Invergowrie, DD2 5DA 13.30pm March 13th WG3 In cereals, such as wheat and barley, crossing overs (CO) are distributed mainly at the end of chromosomes so that centromeric and pericentromeric regions including up to 30% of the genes rarely, if ever, recombine. Thus, substantial proportions of the chromosomes and useful variation that could be exploited in breeding programmes. Therefore an ability to modify the pattern of recombination in these species would have a profound impact on the breeding of these crops. In order to investigate means of altering the patterns of CO in barley, we have utilised SNP technology and cytological procedures, to investigate a collection non-allelic desynaptic barley mutants. All the desynaptic mutants exhibited perturbed meiosis and semi-sterility compared to wild type with some exhibiting an unexpected phenotype during synapsis (Colas et al, 2016). The characterisation of these mutants was only possible through the use of 3D structure illumination microscopy (OMX). Our studies have suggested a tighter control of meiotic progression of chromatin/meiotic axes compared to the model Arabidopsis. In addition to the dissection of the genetic control, preliminary work on the effect of temperature has indicated that recombination frequency and distribution in the male meiocytes is be influenced by environmental factors (Phillips et al, 2015). In this talk, I will present recent work on mutant studies and the effect on temperature on meiosis and recombination in barley and the implications for fertility and the potential use in breeding programmes. Phillips, D., Jenkins, G., Macaulay, M., Nibau, M., Wnetrzak, J., Fallding, D., Colas, I., Oakey, H., Waugh, R., and Ramsay, L. (2015). The effect of temperature on the male and female recombination landscape of barley. New Phytologist. Oct;208(2):421-9 Colas, C., Macaulay, M., Higgins, J.D., Phillips, D., Barakate, A., Posch, M., Armstrong, Chris H. Franklin, F.C.H, Halpin, C., Waugh, R., and Ramsay, L. (2016) A spontaneous mutation in MutL- Homolog 3 (HvMLH3) affects synapsis progression and crossover resolution in the barley desynaptic mutant des10. New Phytol. 212(3):

27 PROTEIN PHOSHATASE 2A PROTECTS SISTER CHROMATID COHESION IN ARABIDOPSIS MALE MEIOSIS I BY MAINTAIN- ING COHESIN SYN1AT CENTROMERES Guoliang Yuan, Nico De Storme, Arp Schnittger, Cathrine Lillo and Danny Geelen Ghent University, Department Plant and Crop, Faculty Bioscience engineering, Coupure links, 653, 9000 Gent, Belgium. danny.geelen@ugent.be 13.50pm March 13th WG3 Meiosis involves two rounds of divisions, first segregating homologous chromosomes (meiosis I) and subsequently, separating sister chromatids (meiosis II). The two-step chromosome distribution process relies on the tight control of cohesion complex that holds the sister chromatids together. To resolve cross overs and separate the homologous chromosomes without dissociating the chromatids, REC8, the alpha kleisin subunit of the cohesion ring, is phosphorylated and subsequently cleaved along the chromosome arms at meiosis I but continues to localize and function at the centromeres. In yeast and vertebrates, centromeric cohesion by REC8 is assured up to metaphase II by protecting it from cleavage by means of phosphatase 2A (PP2A) mediated dephosphorylation. Here, we show that in plants centromeric sister chromatid cohesion until meiosis II also requires the activity of a PP2A type phosphatase complex. The combined absence of the regulatory subunits PP2AB a and PP2AB b leads to premature loss of chromosome cohesion during the first meiotic cell division. Male meiocytes of the pp2ab ab double mutant display premature depletion of SYN1, the plant ortholog of REC8. The PP2AA1 structural and B a regulatory subunit specifically localize to the centromeres up till Metaphase II, supporting a role for the PP2A complex in Syn1 mediated maintenance of centromeric cohesion in plant meiosis

28 PLANT CHROMATIN ORGANIZATION UNDER AMBIENT AND STRESS CONDITIONS Ales Pecinka Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelu 31, CZ-78371, Olomouc, Czech Republic 14.05pm March 13th WG3 Plant nuclear genome is organized into chromatin, which allows for highly controlled packaging of chromosomes in a minimal space. At the same time, chromatin guarantees maintenance of basic genome functions such as transcription and replication. We are interested in understanding the mechanisms of folding chromatin fibers into larger functional domains within interphase nuclei and into condensed chromosomes during cell division. The main goal is to identify nuclear proteins involved in these processes and their chemical modifications. We also aim to understand how abiotic stresses alter chromatin organization and how these changes affect transcription and genome stability. In short term, these processes are necessary for successful completion of a plant life cycle, and contribute to genome evolution in long term

29 DISCOVERING THE EPIGENETIC MEMORY OF STRESS RESPONSE IN MAIZE Forestan C. 1, Farinati S. 1, Pavesi G. 2, Rossi V. 3, Varotto S Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE), University of Padova, Viale dell Università 16, Legnaro (Italy) 2- Department of Biosciences, University of Milan, Via Celoria 26, Milano (Italy) 3- CRA - Unità di Ricerca per la Maiscoltura, Via Stezzano 24, Bergamo (Italy) serena.varotto@unipd.it 14.20pm March 13th WG3 In plants stress perception and adaptation require a variety of physiological, biochemical, transcriptional, and epigenetic responses. Dynamic changes in chromatin structure and concomitant transcriptional variations play a role both in stress response and epigenetic memory mechanisms. Histone marks and gene expression pattern variations could be indeed stably maintained during cell division and sexual reproduction, once the triggering stimulus has been removed. Chromatin may play a pivotal role in somatic memory phenomena, however we are still far from connecting molecular genetics and developmental data around environment and chromatin. In order to understand whether environmental memories are created and eventually propagated, we integrated transcriptional and epigenetic data from maize plants subjected to a mild and prolonged drought stress and after the complete recovery from the stress. We observed that extensive transcriptional changes present soon after the stress application were only partially reset after the recovery stage. Concomitantly, ChIP-Seq analyses revealed a direct correlation between transcriptional variation and H3K4me3 or H3K9ac histone modification enrichment at the majority of stress-regulated gene loci. The facultative heterochromatin mark H3K27me3 was instead associated to a few developmentally regulated genes misregulated by the applied stress. In addition, several stress-responsive genes in which histone marks variations persist after the recovery stage were identified, indicating a form of stress memory. Based on the emerged fundamental role of epigenetic mechanisms in regulating stress response and adaptation we are further evaluating the identified targets in the progeny of the stressed plants and in plants subject to repeated stress pressure Bäurle I Can t rember to forget you: chromatin-based priming of somatic stress responses (2017) Semin Cell Dev Biol. S (16) Forestan C, Aiese Cigliano R, Farinati S, Lunardon A, Sanseverino W, Varotto S. (2016) Stressinduced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis. Sci Rep Jul 27;6:

30 09.10am March 14th WG2 ELUCIDATING THE ROLE OF THE NUCLEOLUS IN THE GLOBAL CHROMATIN ORGANIZATION Picart-Picolo A. 1,2, Carpentier M.- C. 1,2, Picart C. 1,2, Picault N. 1,2, Pontvianne F 1,2 1-CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 58 Avenue P. Alduy, Perpignan, France 2-Univ. de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, 58 Avenue P. Alduy, Perpignan, France fpontvia@univ-perp.fr We are currently studying the mechanisms involved in the chromatin organization and its impact on gene expression using Arabidopsis thaliana as model organism. One of our goals is to help understanding the dynamic of gene positioning within the nucleus, and how this positioning impacts gene expression. The most prominent nuclear compartment is the nucleolus, the site of rrna gene transcription, rrna processing, and ribosome biogenesis. To test for its potential role in gene positioning and expression, we recently isolated nucleoli using fluorescence-activated cell sorting (FACS) and identified Nucleolus-Associated chromatin Domains (NADs) by deep sequencing (Pontvianne et al., 2016). In wild type, NADs are primarily active rrna genes and the entire short arm of chromosome 4 adjacent to them. However, NADs also include genomic regions with heterochromatic signatures enriched in transposable elements (TEs), sub-telomeric regions, and mostly inactive protein- coding genes. Because the RNA polymerase II is depleted from the nucleolus, we now speculate for a possible role of the nucleolus in regulation of gene expression. To test this hypothesis, we are currently identifying NADs under various abiotic stress conditions and in several mutants impaired in chromatinrelated pathways. This will allow us to evaluate the dynamic of NADs, and to understand how their association with the nucleolus is linked to their epigenetic and transcriptional states. We are also developing confocal microscopy approaches to study subnuclear gene positioning. Altogether, these different approaches will allow us to better understand the role of nucleolus on chromatin organization and gene expression. Pontvianne F, Carpentier MC, Durut N, Pavlištová V, Jaške K, Schořová S, Parrinello H, Rohmer M, Pikaard CS, Fojtová M, Fajkus J and Sáez-Vásquez J. (2016) Identification of nucleolus-associated chromatin domains reveals the role of the nucleolus in the 3D organisation of the A. thaliana genome. Cell Reports. August 9 (16) doi: /j.celrep

31 REPLICATION AND TRANSCRIPTION INSIDE THE NUCLEOLUS Martina Dvorácková 1, Berta Raposo 2, Joerg Fuchs 3, Veit Schubert 3, Petr Matula 4, Konstantin Kutashev 1 1- CEITEC MU, Kamenice 753/5, Brno, Czech Republic 2- CBMSO, Nicolas Cabrera 1, Madrid, Spain 3- IPK, Corrensstrasse, Gatersleben, Germany 4- FI MU, Botanická 68a, Brno, Czech Republic dvorackova.martina@gmail.com 09.30am March 14th WG2 The cell biology focused on the spatio-temporal organisation of the plant nucleus has been recently expanded by fast development of efficient labelling methods as well as advanced microscopy approaches. One of the most prominent components of the plant nucleus is represented by nucleolus, a membrane free structure formed around actively transcribed ribosomal genes (rrna genes, rdna), which are crucial for correct proteosynthesis. The cluster of ribosomal genes is organised into repeated units of 10kb with approximately 570 copies per haploid genome, but only a fraction is actively transcribed. Active rdna genes (around 10% in Arabidopsis) are found on the NOR4 and associate to the nucleolus while inactive copies are more condensed, located at NOR2 and distributed in the nucleoplasm. By combination of click it chemistry, structured illumination microscopy, fluorescence in situ hybridisation and in vivo protein labelling approaches we are able to track the replication and transcription inside the nucleolus as well as the distribution of individual histone variants in the actively transcribed rrna genes. We show that nucleolar replication foci labelled by 5- ethynyl-2 -deoxyuridine correspond to the rdna and are organised into net-like structure with intriguing chromatin organisation, containing areas with different condensation status. In addition, rdna transcription is not stopped during its replication. Nucleolar transcripts labelled by 5-ethynyl uridine localise at specific nucleolar sites, with lower level of nucleolar protein fibrillarin. More detailed analyses are planned to determine detailed distribution of replication and transcription in individual nucleolar sub-domains

32 09.45am March 14th WG2 MECHANISMS OF TRANSCRIPTIONAL REGULATION BY ARABIDOPSIS CHROMATIN REMODELER BRM Katarzyna Sosnowska 2, Kamila Jaronczyk 1, Maciej Lirski 2, Maciej Wojcikowski 2, Pawel Siedlecki 1,2, Ruslan Yatusevich 2, Szymon Swiezewski 2, Marta Koblowska 1,2, Andrzej Jerzmanowski 1,2, Rafal Archacki 1,2. 1-Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Poland 2- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, Warsaw , Poland Chromatin remodeling depends on the activity of evolutionarily conserved multimeric complexes such as SWI/SNF, which are thought to act on chromatin template by increasing nucleosome mobility. Genetic studies in Arabidopsis revealed that plant SWI/SNF complexes are critical for proper development, growth, and regulation of hormone-mediated responses (1). We have recently shown that BRM, a major catalytic subunit of the Arabidospsis SWI/SNF complex, controls expression of its target genes by binding to either gene promoters or terminators (2). However, how SWI/SNF works on these genomic sites is not well understood. To further elucidate the molecular mechanisms of BRM activity, we analyzed nucleosome distribution genome-wide in brm null mutant plants. We found that occupancies and positions of -1 and +1 nucleosomes were significantly changed in the mutant, resulting in narrower nucleosome-depleted regions comparing to the wild-type plants. In addition, we show that transcription from a BRM-targeted promoter requires the ATPase activity of BRM, as point catalytic BRM mutants are unable to efficiently activate transcription in the transient transactivation system. Together, our results provide new insights into the mechanisms through which BRM remodeler regulates transcription. 1. Han, S.-K., Wu, M.-F., Cui, S., and Wagner, D. (2015). Roles and activities of chromatin remodeling ATPases in plants. Plant J. 83: Archacki, R., Yatusevich, R., Buszewicz, D., Krzyczmonik, K., Patryn, J., Iwanicka-Nowicka, R., Biecek, P., Wilczynski, B., Koblowska, M., Jerzmanowski, A., Swiezewski S. (2017). Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression. Nucleic Acids Res. 45:

33 ANTISENSE TRANSCRIPTION AND ITS ROLE IN SEED DORMANCY REGULATION Yatusevich, R., Fedak, H., Palusinska, M., Archacki, R., Swiezewski S. Pawinskiego 5a, Warsaw, Poland 10.00am March 14th WG2 Plants have developed multiple strategies to sense the external environment and to adapt growth accordingly. Delay of germination 1 (DOG1) is a major quantitative trait locus (QTL) for seed dormancy strength in Arabidopsis thaliana. DOG1 is extensively regulated, with an cis-acting antisense transcript (asdog1) suppressing its expression in seeds (Fedak et al.,2016). We have also shown that in seedlings antisense transcription allows DOG1 to sense the external environment and respond to drought and ABA plant hormone (Yatusevich et al., 2017). The requirement of asdog1 to respond to ABA and drought suggests that antisense transcription may be an important generic mechanism for sensing and responding to environmental changes in plants. In agreement our work has revealed that the antisense mediated mode of regulation is a generic feature in Arabidopsis genome (Archacki et al., 2017). To show this we profiled the genome-wide binding of a SWI/SNF chromatin remodeling catalytic subunit BRM. Our analysis show that, in addition to genes showing canonical pattern of BRM enrichment near transcription start site, 1600 genes showed a transcription termination site-centered BRM occupancy profile. We found that BRM-bound 3 gene regions have promoter-like features, including presence of TATA boxes and high H3K4me3 levels, and possess high antisense transcriptional activity, which is subjected to both activation and repression by SWI/SNF complex. Our data suggest that control of transcription by antisense is a common mechanism in plants. Archacki, R., Yatusevich, R., Buszewicz, D., Krzyczmonik, K., Patryn, J., Iwanicka-Nowicka, R., Biecek, P., Wilczynski, B., Koblowska, M., Jerzmanowski, A., et al. (2017). Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression. Nucleic Acids Res. 45, Fedak, H., Palusinska, M., Krzyczmonik, K., Brzezniak, L., Yatusevich, R., Pietras, Z., Kaczanowski, S., and Swiezewski, S. (2016). Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript. Proc. Natl. Acad. Sci. U.S.A. 113, E7846 E7855. Yatusevich, R., Fedak, H., Ciesielski, A., Krzyczmonik, K., Kulik, A., Dobrowolska, G., and Swiezewski, S. (2017). Antisense transcription represses Arabidopsis seed dormancy QTL DOG1 to regulate drought tolerance. EMBO Rep. 18,

34 PLANT LAMIN-LIKE PROTEINS AND NON-CG DNA METHYLATION MEDIATE SPECIFIC CHROMATIN TETHERING AT THE NUCLEAR PERIPHERY Bo Hu, Xiuli Bi, Chang Liu Center for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen 72076, Germany 10.45am March 14th WG2 The nuclear envelope not only serves as a physical barrier separating nuclear content from the cytoplasm but also plays critical roles in modulating the proper threedimensional organization of genomic DNA. For both plants and animals, the nuclear periphery (NP) is a functional compartment enriched for heterochromatin. To date, how plants manage to selectively tether chromatin at the NP is unclear. By conducting two-color in situ hybridization experiments on 2C nuclei, we show that in Arabidopsis, specific chromatin positioning at the NP requires plant lamin-like proteins CROWDED NUCLEI 1 (CRWN1) and CRWN4. In metazoans, the epigenetic mark, histone H3 lysine 9 methylation (H3K9me), is required for the anchoring of targeted chromatin at the NP; however, the loss of H3K9me has no effect in this regard in Arabidopsis. Instead, DNA methylation in CHG and CHH contexts turn out to be required for this process. Furthermore, with Hi-C analyses, we show global attenuation of spatial chromatin compartmentalization and chromatin positioning patterns at the NP in both the crwn1 and crwn4 mutants. In summary, our results indicate that specific positioning of chromatin at the NP in Arabidopsis is mediated by lamin-like proteins and non-cg DNA methylation, both of which are unique in plants

35 A POTENTIAL NEW H3K9ME2 METHYLTRANSFERASE ACTING IN THE ENDOSPERM Lauriane Simon 1, Guifeng Wang 1,2, Claudia Köhler am March 14th WG2 1- Swedish University of Agricultural Sciences & Linnean Center for Plant Biology, Uppsala BioCenter, Almas Allé 5, Uppsala, Sweden 2- Present address: Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou , China. The endosperm of most angiosperms is a triploid tissue containing two maternal and one paternal genome. This tissue transfers nutrients to the embryo and is essential for the embryo growth, similar to the placenta in mammals. Genomic imprinting is an epigenetic phenomenon taking place predominantly in the endosperm, causing parental alleles to be differentially expressed. Changing the balance of parental genomes causes deregulation of imprinted genes and endosperm collapse, a phenomenon referred to as triploid block. Mutations in several imprinted genes can bypass the triploid block, revealing the central importance of balanced imprinted gene expression. One strong suppressor of the triploid block is the paternally expressed gene SU(VAR)3-9 HOMOLOG 7 (SUVH7) (Wolff et al., 2015). While the endosperm of triploid seeds has increased deposition of the heterochromatic modification H3K9me2 on transposable elements (TEs), triploid seeds lacking SUVH7 function are depleted of H3K9me2. We furthermore find that SUVH7 interacts with ADMETOS (ADM), a DNAJ protein that previously was shown to cause increased H3K9me2 deposition in triploid seeds (Jiang et al., 2017). Importantly, loss of ADM and SUVH7 affects the same set of TEs, strongly suggesting that they act together to regulate H3K9me2 deposition in the endosperm. SUVH7 has conserved amino acids previously found to be required for the catalytic activity of the H3K9me2 methyltransferases KRYPTONITE, SUVH5, and SUVH6, suggesting that SUVH7 is a functional methyltransferase acting specifically in the endosperm. Jiang, H., Moreno-Romero, J., Santos-González, J., De Jaeger, G., Gevaert, K., Van De Slijke, E., and Köhler, C. (2017). Ectopic application of the repressive histone modification H3K9me2 establishes post-zygotic reproductive isolation in Arabidopsis thaliana. Genes Dev. Wolff, P., Jiang, H., Wang, G., Santos-Gon Alez, J., and Ohler, C. Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

36 A LINKER HISTONE VARIANT DRIVES LIGHT-CONTROLLED HETEROCHROMATIN REARRANGEMENTS IN ARABIDOPSIS Imen Mestiria 1, Gianluca Teano 1, Clara Bourbousse 1, Ouardia Mohamed 1, Lousie O Connor 1, Gerald Zabulon 1, Auguste Genovesio 1, Celia Baroux 2, Chris Bowler 1 and Fredy Barneche 1 1- Institut de biologie de l Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France 2- Plant Developmental Genetics, Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland barneche@biologie.ens.fr 11.20am March 14th WG2 In many plant cells, nuclear and chromatin organization undergo large rearrangements in response to endogenous and environmental signals. Such phenotypic changes of the nucleus are typically orchestrated during cell specialization and adaptation but their functional significance are poorly understood. For example, the sub-nuclear partitioning of silent heterochromatin is subject to extensive variations during post-embryonic cotyledon development, ultimately condensing around the centromeres as conspicuous foci named chromocenters in adult seedlings. We observed that chromocenter formation during cotyledon development is dependent on photoreceptormediated light sensing and downstream signal pathways involving DET1 and COP1. This photomorphogenic switch leads to a strong reduction in chromatin mobility. It also involves a 2-fold increase in RNA Polymerase 2 activity, indicating a transition from partially quiescent nuclei in etiolated cotyledons to a more active transcriptional status in photosynthetic ones (Bourbousse et al, 2012). We further unveiled that light-dependent heterochromatin dynamics are largely driven by a tight control of expression and stability of the linker histone H1.3, which contrasts the crucial role played by canonical linker histones H1.1 and H1.2 in heterochromatin condensation. When induced by light signaling, H1.3 may compete with H1.1/H1.2 isoforms to trigger a wide relaxation of heterochromatin. These findings unveil how a specific environmental signal is translated in a molecular determinant of nuclear organization. Bourbousse C, Mestiri I, Zabulon G, Bourge M, Formiggini F, Koini MA, Brown SC, Fransz P, Bowler C, Barneche F. (2015) Light signaling controls nuclear architecture reorganization during seedling establishment. PNAS. 112(21):E

37 TRANSGENE SILENCING IN 3D HOW A CHROMOSOMAL KNOT CAN INACTIVATE FOREIGN DNA ELEMENTS Stefan Grob and Ueli Grossniklaus Institute of Plant and Microbial Biology, University of Zürich sgrob@botinst.uzh.ch 11.35am March 14th WG2 Cells require elaborate mechanisms to efficiently pack chromosomes in the nucleus, while still allowing access to the genetic information. In addition to packaging, three-dimensional (3D) chromosome architecture is tightly linked to epigenetic processes and transcriptional activity. Despite the rapid progress in the field, well-established cases of functional relationships between transcription and 3D chromatin architecture remain rare. We previously identified a 3D chromatin structure in Arabidopsis termed the KNOT, in which ten genomic regions (KEEs) physically contact each other. KEEs are preferred transposon landing sites and exhibit heterochromatic features. Here we show that KEEs are also involved in the silencing of transgenes. Transgenes integrated in the genome can fold towards the KNOT, coinciding with their transcriptional silencing. Thus, transgene integration can lead to significant perturbation of 3D chromosome architecture. Interestingly, genomic regions adjacent to the insertion sites are not subjected to silencing, despite their dislocation within the nucleus. This novel silencing mechanism, termed KNOT-linked Silencing (KLS) may act independently of previously described silencing mechanisms, as we cannot observe any significant contribution of small RNAs and DNA methylation. KLS is heritable across generation and shows trans-silencing effects, as the introduction of KNOT-silenced transgenes can lead to the silencing of previously active transgenes. In summary, we describe a potent and novel silencing mechanism involving 3D folding of chromosomes

38 List of Posters WG1.1- Spatial Euchromatin Structure And Interactive Image Analysis Till Bey (University of Amsterdam) WG1.2- SUN proteins and their interactors at the plant nuclear envelope: Katja Graumann (Oxford Brookes University) WG1.3- Studying Transcription Coordination At The Single Locus Level Using Single Molecule RNA Fish Stefanie Rosa (Swedish University of Agricultural Sciences) WG1.4- Improvement of 3D-image analysis tools and pilot study to use OMERO as a multi-purpose platform to analysis & share datasets Mariamawit Ashenafi (University of Zürich) WG2.1- Correlation between nuclear shape and rigidity in Arabidopsis Marie-Edith Chabouté (Université de Strasbourg) WG2.2- Identification Of Novel Components Of The Polycomb Pathway In Arabidopsis Sara Farrona (NUI Galway) WG2.3- Nuclear Dynamics In Arabidopsis Valérie Gaudin (INRA Versailles) WG2.4- Flow Cytometry Is A Key Tool To Analyze The Organization Of Nuclear Chromatin Hana Jerábková (IEB Olomouc) WG2.5- Role Of Epigenetic Regulation At The Nuclear Envelope In Arabidopsis Kalyanikrishna (Freie Universität Berlin) WG2.6-Targeting of A. thaliana KNL2 to centromeres depends on the conserved CENPC-k motif of its C-terminus Inna Lermontova (Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben) List of Posters WG2.7- Auxin Promotes Histone Exchange During Root Development Meschichi Anis (Swedish University of Agricultural Sciences) WG2.8- PWO1: a putative missing link between PcG-mediated gene repression and nuclear lamina. Pawel Mikulski (John Innes Centre, Norwich) WG2.9- Role Of PRC2 During Embryogenesis And Embryo-To-Seedling Transition Iva Mozgová (Centre Algatech, Czech Republic & University of South Bohemia WG2.10- Characterisation Of Plant Mobile Domain Proteins Nicolau Mélody (University of Perpigan) WG2.11- Histone H3.3 Deposition Pathways In Arabidopsis thaliana Aline Probst (Université Clermont Auvergne) WG2.12- The Use Of Pseudotrypsin For The Identification Of Proteins From Barley Nuclei Marek Šebela (IEB Olomouc) WG2.13- Exploring Chromatin Mobility In Plant Nuclei With Dramatically Distinct Chromatin Architecture And Heterochromatin Condensation Status. Gianluca Teano (CNRS Paris) WG3.1- Epigenetic Modulation Of Recombinant Protein Production In Plant Cell Cultures Rita Abranches (Plant Cell Biology Lab, Oeira, Portugal) WG3.2- New Breeding Efforts For Climate Smart Oil Crops Sandra Cvejic (Institute of Field and Vegetable Crops, Serbia) WG3.3- Dissection Of Genomic Architecture Of Complex Traits And Their Phenotypic Plasticity In Tetraploid Wheat Under Drought Stress Andrii Fathiukha (University of Haifa) 74 75

39 List of Posters WG3.4- Plant cell wall integrity maintenance and immune signaling cooperate to control stress responses in Arabidopsis thaliana Thorsten Hamann (Norwegian University of Science and Technology, Trondheim, Norway) WG3.5- Elucidating the role of a bromoidomain protein enabling viroid and satellite virus infectivity Kalantidis K (University of Crete) WG3.6- The Characterization Of Epigenetic Regulators During Seed Development And Abiotic Stress-Response In Different Barley Cultivars Aliki Kapazoglou (INAB, CERTH, Thessaloniki) WG3.7- A Meta-Analysis Of The Tobacco Pollen Transcriptome. Actively Translated And Stored Nuclear Genes During Pollen Development Christos Michailidis (Laboratory of Pollen Biology, IEB Prague) WG3.8- Comparative Phenotypic And Metabolic Analysis Of Helianthus Species For Improved Stress Resilience Dragana Miladinovic (Institute of Field and Vegetable Crops, Serbia) WG3.9- Reproductive Traits Study For Improvement Of Local Viticulture In Armenia Anita Nebish (Yerevan State University, Armenia) List of Posters WG3.13- Response Of Sugar Beet Genotypes To In Vitro Induced Water Deficit Ksenija Ajdukovic ((Institute of Field and Vegetable Crops, Serbia) WG3.14- Analysis Of Plant Genome Structure Using Molecular Cytogenetics Tools Ahmet L. Tek (NiTde Ömer Halisdemir University, Turkey) WG3.15- Nuclear Changes Associated With Stress Induced Microspore Embryogenesis M. P. Vallés (Aula Dei Experimental Station, Zaragoza) WG3.16- Histone H2A (de)ubiquitination affects the function of the circadian clock in Arabidopsis thaliana László Kozma-Bognár (IPB, Szeged) No Poster supplied. WG4.1- HPC and GPGPU for Large-Scale Image Processing Cédric Charière Fiedler (Campus Universitaire des Cézeaux) WG4.2- AuBi platform for biologists and bioinformaticians at UCA Mesocentre Nadia Goué (Platform Auvergne Bioinformatics, Clermont Auvergne University WG3.10- Fine Organization Of Genomic Regions Tagged To The 5S Rdna Locus Of The Bread Wheat 5B Chromosome Elena A. Salina (Institute Of Cytology And Genetics Novosibirsk) WG3.11- Novel Approaches To Analysing Ribosomal Rna Multigene Loci In Barley Simkova, H (IEB Olomouc) WG3.12- Seedlings Growth And Transcriptional Responses To Salt And Drought Stress Of Medicago Sativa L, Medicago Arborea L. And Their Hybrid (Alborea) Eleni Abraham (Aristotle University of Thessaloniki) 76 77

40 Poster WG1.1 SPATIAL EUCHROMATIN STRUCTURE AND INTERACTIVE IMAGE ANALYSIS Till Bey and Paul Fransz Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands Poster WG1.2 SUN PROTEINS AND THEIR INTERACTORS AT THE PLANT NUCLEAR ENVELOPE Bisa Andov, Gwen Detourne, David Evans, Katja Graumann Dept of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK In the interphase nucleus of Arabidopsis thaliana constitutively silenced heterochromatin appears as highly condensed chromocenters. In contrast, most genes are located in the less compacted euchromatin. We are investigating if there exists a general functional segregation of genes into distinct spatial domains. For this we have developed a setup for staining multiple targets in 3D preserved nuclei to image euchromatin structure at the submicrometer scale. DNA, RNA polymerase II and different histone modifications exhibit characteristic distribution patterns throughout euchromatin. For some marks only very subtle but reproducible variations in staining density can be observed. Additionally, we are using FISH to visualize specific DNA sequences and their colocalization with euchromatic domains. These multichannel images are very rich datasets and pose several challenges to analysis. We have developed an interactive program, Texel, to help constructing image analysis pipelines and to explore the extracted data. Texel bridges the gap between advanced analysis libraries and an accessible, visual approach to image analysis. Building on the rich Python ecosystem for scientific computing, it is based on established libraries and is quickly extensible with new functionality. A key focus lies on modular, reusable pipelines that are abstracted from the underlying code that can easily be shared. Integrated visualization allows inspection of multidimensional images and exploration of data. Bey, TD, Koini, M, Fransz, P (2018): Fluorescence in situ hybridization (FISH) and immunolabeling on 3D preserved nuclei. Plant Chromatin Dynamics: Methods and Protocols, Methods in Molecular Biology, vol Our group is interested in the protein composition and functions of the plant nuclear envelope (NE). We use Arabidopsis and tobacco plants mostly for confocal microscopy. Techniques such as fluorescence recovery after photobleaching (FRAP) and acceptor photobleaching fluorescence resonance energy transfer (apfret) allow us to dissect protein interactions and behavior in living plant tissue. Specifically, we are interested in the composition and function of nucleo-cytoskeletal bridging complexes at the NE. To this end we have previously identified plant SUN proteins and dissected their interactions with plant- specific KASH proteins. We ve also identified a novel group of plant-specific NE proteins called NEAPs. We are interested in characterizing the NEAPs further in terms of their functions and putative involvement in bridging complexes. Poulet, A., Probst, A.V., Graumann, K., Tatout, C. and Evans, D.E., (2016), Exploring the Evolution of the Proteins of the Plant Nuclear Envelope., Nucleus, 19, 1-14 Pawar V., Poulet A., Detourne G., Tatout C, Vanrobays E., Evans DE. and Graumann K., (2016), A novel family of plant nuclear envelope associated proteins., Journal of Experimental Botany, 67, (19), Smith S., Galinha C., Desset S., Tolmie AF., Evans DE., Tatout C. and Graumann K., (2015), Marker Gene tethering by nucleoporins affects gene expression in plants., Nucleus, 6, (6), Varas J., Graumann K., Osman K., Pradillo M., Evans D.E., Santos J.L. and Armstrong S.J., (2015), Absence of SUN1 and SUN2 proteins in Arabidopsis thaliana leads to a delay in meiotic progression and defects in synampsis and recombination, The Plant Journal, 81, Graumann K., Vanrobays E., Tutois S., Probst A.V., Evans D.E. and T atout C., (2014), Characterization of two distinct subfamilies of SUN-domain proteins in Arabidopsis and their interactions with the novel KASH-domain protein AtTIK, Journal of Experimental Botany, 65, (22), Zhou X., Graumann K., Wirthmueller L., Jones J.D.G. and Meier I., (2014), Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants, JCB, 205, (5), Graumann K., (2014), Evidence for LINC1-SUN associations at the plant nuclear periphery, PLOS ONE, 9, (3), e

41 Poster WG1.3 STUDYING TRANSCRIPTION COORDINATION AT THE SINGLE LOCUS LEVEL USING SINGLE MOLECULE RNA FISH Stefanie Rosa Swedish University of Agricultural Sciences, Uppsala Sweden Poster WG1.4 STSM PROJECT: IMPROVEMENT OF 3D-IMAGE ANALYSIS TOOLS AND PILOT STUDY TO USE OMERO AS A MULTI- PURPOSE PLATFORM TO ANALYSIS & SHARE DATASETS Mariamawit Ashenafi (UZH), Dr. Célia Baroux(UZH), Pierre Pouchin (GReD), Sophie Desset (GReD), Prof. Christophe Tatout (GReD) Stefanie.rosa@slu.se The recent developments in genomics and bioinformatics have unveiled an unexpected complexity of the eukaryotic transcriptome. A surprise that emerged is the prevalence of transcription on antisense orientation of protein-coding genes. While the genome- wide role for non-coding antisense transcription is subject of obvious interest, its sheer existence can come at a cost for genome integrity. RNA Polymerases (RNAPII) transcribing opposite strands cannot bypass each other and head-to- head RNAPII collisions are likely to be harmful for the cells leading to gene blockage, backtracking or DNA damage. With the pervasive nature of antisense transcription on eukaryotic genomes, this raises the question of what are the mechanisms in place to prevent RNAPII collisions. Most studies of antisense transcription rely on methods that measure average behaviors in cell populations, lacking resolution to observe the effects of non-coding antisense transcripts at the cellular level. Using a single molecule RNA FISH (smfish) approach (Duncan et al., 2016) we have recently demonstrated one locus in Arabidopsis thaliana, where sense/antisense transcription can occur on a strictly coordinated and mutually exclusive fashion (Rosa et al., 2016). We are now hypothesizing that this may be a general feature among eukaryotic genomes that has evolved to avoid RNAPII collisions, and we are currently investigating the occurrence of mutually exclusive transcription at sense/antisense gene pairs and its molecular regulation. The dynamic transition between euchromatin and heterochromatin state of the genomic DNA has implications for the regulation of key processes such as transcription, replication and DNA repair. Moreover, several studies have shown correlation between spatial organization of genome and transcription activation or silencing for different species, especially in relation to nuclear periphery and chromocenters. This is why during this project we will explore OMERO s cross platform image processing feature and enhance it to detect and segment nuclear surface, chromocenters, and nucleolus of plant nucleus. This will allow automated comparison between different nuclear samples. We will also establish a protocol for high resolution 3D plant nuclei image acquisition using confocal microscopy, and provide images on OMERO repository. Rosa S, Duncan S, Dean C. (2016) Mutually exclusive sense antisense transcription at FLC facilitates environmentally induced gene repression. Nature Communications 7, doi: / ncomms Duncan S, Olsson T, Hartley M, Dean C and Rosa S. (2016) Imaging single RNA transcripts in plants reveals cell-to-cell variability in gene transcription. Plant Methods 12:13, doi: /s x 80 81

42 Poster WG2.1 CORRELATION BETWEEN NUCLEAR SHAPE AND RIGIDITY Rituparna Goswami 1,2, Atef Asnacios 3, Stéphanie Graindorge 1, Guy Houlné 1, Pascale Milani 4, Olivier Hamant 2, Marie-Edith Chabouté 1 IDENTIFICATION OF NOVEL COMPONENTS OF THE POLYCOMB PATHWAY IN ARABIDOPSIS Eduardo March 1, Daniel Schubert 2 and Sara Farrona 1 Poster WG Institut de biologie moléculaire des plantes, UPR2357 CNRS, Université de Strasbourg, 2- Laboratoire Reproduction et Développement des Plantes, INRA, CNRS, UCBL1, ENS de Lyon 3- Laboratoire Matières et Systèmes Complexes, Université Paris-Diderot and CNRS UMR 7057, Sorbonne Paris Cité, 4- BioMeca, ENS de Lyon marie-edith.chaboute@ibmp-cnrs.unistra.fr Mechanical signals play an important role in biological processes at both cellular and organism levels. In plants, external mechanical stimuli, such as wind, lead to the induction of specific mechanosensitive genes, such as TOUCH genes (1). Plant cells also respond to internal mechanical stress. For instance, at the Arabidopsis shoot apex, emergence of new organs leads to mechanical constraints, that affect the microtubular cytoskeleton (2) and gene expression (3). Although the mechanotransduction pathways remains ill-known in plants, nucleus shape and architecture may be an important contributor to mechanosensing and transcription. Here we first investigated whether impaired nuclear shape correlates with modified nuclear rigidity in root apical meristems. As a model system, we compared wild type and deformed gip1gip2 nuclei mutants. GIP1 and GIP2 are key nuclear envelope proteins, involved in both microtubule and chromatin organization (4,5,6). Using both atomic force microscopy and micro-rheometry, we found that nuclei of gip mutants are stiffer compared to WT. In addition transcriptomic analyses show that gip1gip2 are constitutively stressed, with the induction of several genes linked to mechanotransduction and stress response. This suggests that GIP proteins, together with other actors, may contribute, to the mechanical stress response at the nuclear envelope in plants (7). (1) Braam J (2005) In touch: plant responses to mechanical stimuli.new Phytol. 165, (2) Hamant, O et al (2008). Developmental patterning by mechanical signals in Arabidopsis. Science 322, (3) Landrein, B et al (2015). Mechanical stress contributes to the expression of the STM homeobox gene in Arabidopsis shoot meristems. Elife 4, e (4) Janski, N et al (2012). The GCP3-interacting proteins GIP1 and GIP2 are required for γ-tubulin complex protein localization, spindle integrity, and chromosomal stability. Plant Cell 24, (5) Batzenschlager, M et al (2013). The GIP gamma-tubulin complex-associated proteins are involved in nuclear architecture in Arabidopsis thaliana. Front Plant Sci 4, 480. (6) Batzenschlager, M et al (2015). Arabidopsis MZT1 homologs GIP1 and GIP2 are essential for centromere architecture. Proc. Natl. Acad. Sci. U.S.A.112, (7) Fal, K et al (2017). Nuclear envelope: a new frontier in plant mechanosensing? Biophys Rev 9, Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway, Galway, Ireland 2- Institut of Biologie, Freie University Berlin, Berlin, Ireland sara.farrona@nuigalway.ie Polycomb Group (PcG) proteins are master regulators of cell fate and development through the epigenetic regulation of gene expression. Although PcG proteins are well conserved in and their molecular functions have been characterised, it is still unclear how PcG proteins are regulated. We have identified PWWP-DOMAIN INTERACTOR OF POLYCOMBS 1 (PWO1) as a new component of the PcG pathway (Hohenstatt et al., 2018). PWO1 belongs to a small subfamily of three PWWP proteins highly conserved through the plant kingdom. Single pwo1 mutants have a very mild phenotype, but mutants affected in the three genes of the PWO subfamily are strongly impaired in development. The PWWP domain is required for the nuclear localization of PWO1 in speckles where it recruits PcG proteins. In addition, the PWWP domain interacts with histone (H3) peptides, which is reduced by a point mutation in a highly conserved residue of this domain and blocked by phosphorilation of H3S28. To further characterise PWO1 s functions, we have analyzed PWO1 putative complex(es) in planta by immunoprecipitation (IP) experiments and subsequent liquid chromatography-mass spectrometry (LC-MS/MS). The experiments yielded more than one hundred potential PWO1 interactors. Among them, we have focused on the two most abundant PWO1 interactors: a PHD containing protein and a ubiquitin protease. Here, we will present confocal microscopy data for the nuclear localisation of these two PWO1 interactors and molecular data that further link them to the PcG pathway. Hohenstatt, M.L., Mikulski, P., Komarynets, O., Klose, C., Kycia, I., Jeltsch, A., Farrona, S., and Schubert, D. (2018). PWWP-DOMAIN INTERACTOR OF POLYCOMBS11 interacts with Polycombgroup proteins and histones and regulates Arabidopsis flowering and development. Plant Cell

43 Poster WG2.3 Poster WG2.4 NUCLEAR DYNAMICS IN ARABIDOPSIS Stefania Del Prete, Javier Arpón, Kaori Sakai, Philippe Andrey, Valérie Gaudin INRA, UMR1318-AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), INRA- Centre de Versailles-Grignon, Route de St-Cyr, F Versailles Cedex, France The interphase cell nucleus is an extraordinarily complex, ordered, and dynamic organelle. In the last decade, remarkable progress has been made in deciphering the functional organization of the cell nucleus, and intricate relationships between genome functions and various nuclear compartments have been revealed (Del Prete et al., 2014). We aim at deciphering the organizational rules of the Arabidopsis cell nucleus by using 3D imaging, spatial statistics and modeling approaches (Andrey et al., 2010; Arpon et al., 2017). Andrey, P., Kieu, K., Kress, C., Lehmann, G., Tirichine, L., Liu, Z., Biot, E., Adenot, P.G., Hue- Beauvais, C., Houba-Herin, N., Duranthon, V., Devinoy, E., Beaujean, N., Gaudin, V., Maurin, Y., and Debey, P. (2010). Statistical analysis of 3D images detects regular spatial distributions of centromeres and chromocenters in animal and plant nuclei. PLoS Comput Biol 6, e FLOW CYTOMETRY IS A KEY TOOL TO ANALYZE THE ORGANIZATION OF NUCLEAR CHROMATIN Hana Jerábková 1, Beáta Petrovská 1, Jan Vrána 1, Marek Šebela 2, Veronika Burešová 1, Ales Pecinka 1, Jaroslav Doležel 1 1- Institute of Experimental Botany (IEB), Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelu 31, CZ-78371, Olomouc, Czech Republic 2- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelu 11, CZ-78371, Olomouc, Czech Republic jerabkova@ueb.cas.cz The organization of nuclear chromatin is dynamic and undergoes changes during cell cycle, tissue differentiation and in response to the environment. The ability to isolate large quantities of intact nuclei is critical for the functional analyses of plant chromatin. We will show that flow cytometry (FCM) represents a powerful and versatile technique, which provides a launching pad for many types of chromatin assays. FCM is fast and effective approach for the estimation of genome size, analysis of cell cycle kinetics and sorting cells and their organelles. Arpon, J., Gaudin, V., and Andrey, P. (2017). A method for testing random spatial model on nuclear object distributions. In Methods in Molecular Biology: Plant Chromatin Dynamics, B. Bemer and C. Baroux, eds (Springer NY. Del Prete, S., Arpon, J., Sakai, K., Andrey, P., and Gaudin, V. (2014). Nuclear architecture and chromatin dynamics in interphase nuclei of Arabidopsis thaliana. Cytogenetic and Genome Research 143, It enables isolation of nuclei in G1, S and G2 phases of cell cycle and, in some species, also condensed mitotic chromosomes. We will demonstrate how a combination of FCM with proteomic analysis allows high-throughput identification of nuclear proteins in barley. Furthermore, we will show examples how flow-sorted nuclei and chromosomes can be used for various microscopic and molecular applications

44 Poster WG2.5 ROLE OF EPIGENETIC REGULATION AT THE NUCLEAR ENVELOPE IN ARABIDOPSIS Kalyanikrishna 1, Pawel Mikulski 1,2,3, Mareike Hohenstatt 3 and Daniel Schubert 1,3 1- Institute of Biology, Freie Universität Berlin, Germany 2- John Innes Centre, Norwich, UK 3- Institute for Genetics, Heinrich-Heine-University Düsseldorf, Germany kalyani@zedat.fu-berlin.de Polycomb group (PcG) proteins play a crucial role in the development of a wide range of eukaryotes, including plants and animals. One of the PcG protein complexes, Polycomb Repressive Complex 2 (PRC2), promotes repressive chromatin formation via tri-methylation of lysine-27 on histone H3 (H3K27me3) (Köhler and Villar, 2008). From previous studies in the lab, we characterized a novel chromatin protein family in Arabidopsis, PWWP INTERACTOR OF POLYCOMBS1 (PWO family) which consists of three members. PWO1 is found to be a plant specific interactor of PRC2 and histone H3 (Hohenstatt et al., 2018). Co-immunoprecipitation experiment coupled with mass spectrometry revealed 109 putative PWO1 interactors (Mikulski et al., 2017) and ~60% of those overlap with components of crude plant nuclear envelope enriched fraction (Sakamoto and Takagi, 2013). Presence of nuclear lamina associated components, especially CROWDED NUCLEI 1(CRWN1) - a coiled coil analog of lamin proteins in Arabidopsis - gained attention as it has prominent role in maintaining nuclear morphology (Wang et al., 2013) and chromocenter organization (Dittmer et al., 2007). Further investigation on PWO1- CRWN1 showed a physical and genetic interaction and similar set of regulated genes, thus provide a putative link between PRC2-mediated gene repression and the nuclear periphery in plants (Mikulski et al., 2017). The current project I am working on is a comprehensive functional analysis of the three PWO family proteins and extended studies on CRWN proteins and PWO1 interactors identified in the nuclear envelope enriched fraction to decode further strategies in PRC2 mediated gene silencing at the nuclear periphery. Poster WG2.6 TARGETING OF A. THALIANA KNL2 TO CENTROMERES DEPENDS ON THE CONSERVED CENPC-K MOTIF OF ITS C-TERMINUS Michael Sandmann 1, Paul Talbert 2, Dmitri Demidov 1, Markus Kuhlmann 1, Twan Rutten 1, Udo Conrad 1 and Inna Lermontova 1 1- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, D Stadt Seeland, Germany 2- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Centromeres contain specialized nucleosomes at which histone H3 is replaced by the centromeric histone H3 variant cenh3 that is required for the assembly, maintenance, and proper function of kinetochores during mitotic and meiotic divisions. In higher eukaryotes, positions of cenh3 incorporation and kinetochore assembly do not depend on specific DNA sequences, but are rather determined epigenetically. We have identified a KNL2 (Kinetochore Null 2) of A. thaliana that is involved in the recognition of centromeres and centromeric localization of cenh3 similar to its homologues of C. elegans and mammals. KNL2 homologues identified so far contain a conserved SANTA domain, possibly involved in protein-protein interactions, at the N-terminus, but only some of them contain SANT/Myb (DNA binding) domain at the C-terminus. Our recent study revealed a cenh3 nucleosome-binding CENPC-k motif at the C-terminus of A. thaliana KNL2, which is conserved among a wide spectrum of eukaryotes. Centromeric localization of KNL2 is abolished by deletion of the CENPC-k motif and by mutating single conserved amino acids, but can be restored by insertion of the corresponding motif of A. thaliana CENP-C. We showed by electromobility shift assay (EMSA) that the C-terminus of KNL2 binds DNA sequence-independently and interacts with the centromeric pal1 transcripts in vitro. Chromatin immunoprecipitation with anti-knl2 antibodies indicated that in vivo KNL2 is preferentially associated with the centromeric repeat pal1. Complete deletion of the CENPC-k motif did not influence its ability to interact with DNA in vitro. Therefore, we suggest that KNL2 recognizes centromeric nucleosomes, similar to CENP-C, via the CENPC-k motif and binds adjoining DNA. Dittmer, T. A et al (2007). LITTLE NUCLEI genes affecting nuclear morphology in Arabidopsis thaliana. Plant Cell 19, Hohenstatt, L.M et al (2018). PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 interacts with Polycomb-group proteins and histones and regulates Arabidopsis flowering and development. Plant Cell 30 (1), Köhler, C and Villar, C.B. (2008). Programming of gene expression by Polycomb group proteins. Trends Cell Biol. 18, Mikulski, P et al (2017). PWWP INTERACTOR OF POLYCOMBS (PWO1) links PcG-mediated gene repression to the nuclear lamina in Arabidopsis. biorxiv preprint,

45 Poster WG2.7 AUXIN PROMOTES HISTONE EXCHANGE DURING ROOT DEVELOPMENT Meschichi Anis 1, Grebe Markus 2, Stefanie Rosa 1 1- Swedish University of Agricultural Sciences, Uppsala Sweden 2- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany. Anis.meschichi@slu.se Unlike animals, plants show indeterminate growth, requiring continuous production of new cells from actively dividing meristems. For meristem maintenance a tight control of cell division and differentiation is required. While much progress has been made on the genetic network controlling this balance little is known about the intrinsic properties of meristematic cells. Our previous work has highlighted that changes in global histone mobility are involved in the maintenance of a balance between cell division and cell differentiation in the root meristem of Arabidopsis thaliana (Rosa et al., 2014). The establishment and maintenance of the root meristem has been shown to result from the balance between the plant hormones auxin and cytokinin. Here, we show that the plant hormone auxin increases histone mobility and acetylation but is unable to promote an increase in meristem size when HAG1 (histone acetyltransferase of the GNAT family 1) activity is disrupted. Our results show that meristematic cells are characterized by mobile histones and that auxin plays a role on this process by directly affecting histone acetylation levels. Rosa S, Ntoukakis V, Ohmido N, Pendle A, Abranches R and Shaw P. (2014) Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single cell level. The Plant Cell 26, Poster WG2.8 PWO1: A PUTATIVE MISSING LINK BETWEEN PCG-MEDIATED GENE REPRESSION AND NUCLEAR LAMINA. Pawel Mikulski 1, Mareike Hohenstatt 2, Sara Farrona 3, Cezary Smaczniak 4, Kerstin Kaufmann 4, Gerco Angenent 5, Daniel Schubert 6 1- Cell and Developmental Biology, John Innes Centre, Norwich, UK 2- Department of Biology, Henrich Heine University, Duesseldorf, Germany 3- School of Natural Sciences, National University of Ireland, Galway, Ireland 4- Institute of Biology, Humboldt University, Berlin, Germany 5- Lab. of Molecular Biology, Wageningen University, Netherlands 6- Institute of Biology, Free University of Berlin, Berlin, Germany pawel.mikulski@jic.ac.uk The components of Polycomb Repressive Complex 2 (PRC2), as the members of Polycomb- group (PcG) proteins, control developmental transitions and cause epigenetic gene repression by tri-methylation of lysine 27 on histone H3 (H3K27me3) in plants and animals. Polycomb pathway has been extensively studied in respect to its components biochemistry and transcriptional effect on its target genes, canonically implying one layer of gene regulation. However, recent discoveries suggest that PcG-mediated gene repression comprises also spatial organization of the chromatin in the nucleus ([1]). Specifically, PcG- mediated repression was shown to be associated with nuclear periphery in mammals and invertebrates ([2],[3]); however such association remained largely unexplored in plant species. Here I present PWWP-DOMAIN INTERACTOR OF POLYCOMBS 1 (PWO1), a plant- specific protein of Arabidopsis thaliana, that we identified as a novel component of PcG pathway. We showed that PWO1 interacts with PRC2 members, regulates transcription of similar set of genes as PRC2 and is required for full H3 and H3K27me3 deposition at several PcG targets ([4]). Interestingly, PWO1 co-immunoprecipitates with proteins enriched at the nuclear lamina (NL), a structural mesh residing in peripheral regions of the nucleus, including CROWDED NUCLEI (CRWN) family members. Moreover, PWO1 controls nuclear size, similarly to core NL mutants, shows genetic interaction with selected CRWN gene and impacts expression of CRWN-regulated targets. Overall, I propose that PWO1 serves as a putative plant-specific link between nuclear lamina and PcG-mediated gene repression

46 Poster WG2.9 ROLE OF PRC2 DURING EMBRYOGENESIS AND EMBRYO-TO-SEEDLING TRANSITION Helena Hönig Mondeková 1, Tomáš Konecný 1, Rafael Muñoz-Viana 1, Juan Santos-Gonzales 2, Lenka Bucinská 1, Martin Tichý 1, Roman Sobotka 1, Jirí Kubásek 1, Jirí Šantrûcek 1, Radek Kana 1, Claudia Köhler 2, Lars Hennig 2, Iva Mozgová 1 1- Centre Algatech Institute of Microbiology CAS, Trebon, Czech Republic & University of South Bohemia in Ceské Budejovice, Czech Republic 2- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden mozgova@alga.cz or iva.mozgova@gmail.com Polycomb Repressive Complex 2 (PRC2) governs major developmental transitions in Arabidopsis thaliana. While PRC2 is required during the embryo-to-seedling transition, it seems to be dispensable in early embryogenesis (Bouyer et al., 2011). Presence of H3K27me3 in the Arabidopsis embryo nevertheless raises the question whether PRC2 plays a role during embryogenesis and how remodeling of the H3K27me3 distribution contributes to the embryo-to-seedling transition. I will present our ongoing work focused on two questions: First, what is the role of PRC2 during embryogenesis, and second, how does PRC2 ensure stable developmental and metabolic transition during seedling establishment. To address the role of PRC2 during embryogenesis, we profiled the transcriptome and H3K27me3 distribution of wild-type zygotic and somatic embryos, embryo-derived non-embryogenic callus and seedlings, as well as the transcriptome of clf swn somatic embryos and seedlings (Mozgová et al., 2017). We identified distinct sets of H3K27me3-modified genes specifying the individual developmental samples, but also genes targeted by PRC2 across all the samples that are mostly related to metabolic processes. Comparing the gene expression in the wild-type and clf swn samples, we identify pathways that require PRC2 activity to prevent their ectopic activation. For addressing the function of PRC2 in the embryo-to-seedling transition, we focus on early post-germination stages of development and combine genome-wide profiling of source and sink tissue with biochemical and biophysical approaches to identify the upstream-most causes of growth defects in PRC2 mutant seedlings. By this, we aim to pinpoint pathways governed by PRC2 that stably establish vegetative growth and development. CHARACTERIZATION OF PLANT MOBILE DOMAIN PROTEINS Nicolau Mélody, Descombin Julie, Picault Nathalie and Moissiard Guillaume. Laboratoire Genome et Developpement des Plantes. 58, Avenue P. Alduy, Perpignan melody.nicolau@univ-perp.fr Poster WG2.10 In Arabidopsis thaliana, transposable elements (TEs) are targeted by different epigenetic pathways to ensure genome integrity. DNA methylation and histone modifications contribute to the regulation of gene expression and silencing of TEs. In addition, plants have developed synergistic pathways that converge towards TE silencing, such as the Microrchidia (Morc) and the Morpheus Molecule 1 (MOM1) pathways (Amedeo et al., 2000 ; Moissiard et al., 2012, 2014). Recently, MAINTENANCE OF MERISTEM-LIKE 1 (MAIL1) and its close homolog MAINTENANCE OF MERISTEM (MAIN) were described as new actors involved in the silencing of TEs (Ikeda et al., 2017). Originally identified as genes required for genome integrity in the meristems (Wenig et al., 2013 ; Ühlken et al., 2014), the MAIN and MAIL1 genes belong to a multigene family including MAIL2 and MAIL3. The MAIN/MAIL proteins carry a Plant Mobile Domain (PMD) of unknown function, which can be fused to some transposase domains of the MULE and Gypsy TE families (Babu et al., 2006). Using a forward genetic approach, we have also identified MAIN as a gene required for the silencing of the several TEs. The aim of my PhD is to decipher the mode of action of PMD proteins using molecular (Western Blot, RT-qPCR,..), NGS (RNA-seq, BS-seq, ChIP-seq,..), biochemical (IPMS, coip, ) and microscopic (IF, confocal analyses) approaches. Bouyer, D., Roudier, F., Heese, M., Andersen, E.D., Gey, D., Nowack, M.K., Goodrich, J., Renou, J.P., Grini, P.E., Colot, V., et al. (2011). Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet 7, e Mozgová, I., Muñoz-Viana, R., and Hennig, L. (2017). PRC2 represses hormone-induced somatic embryogenesis in vegetative tissue of Arabidopsis thaliana. PLOS Genet. 13, e

47 Poster WG2.11 HISTONE H3.3 DEPOSITION PATHWAYS IN Arabidopsis thaliana C. Duc 1, M. Benoit 1, G. Détourné 1,2, L. Simon 1, A. Poulet 1,2, M. Jung 3, A. Veluchamy 4,5, D. Latrasse 4, N. Corre 4, S. Le Goff 1, S. Cotterell 1, C. Tatout 1, M. Benhamed 4,5 and A. V. Probst 1 1- Université Clermont Auvergne, CNRS, Inserm, GReD, F Clermont- Ferrand, France 2- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK. 3- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France 4- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris- Sud, Université Evry, Université Paris-Saclay, Orsay, France 5- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia aline.probst@uca.fr Histones are essential components of the nucleosome, the major subunit of chromatin that structures linear DNA molecules and regulates access of other proteins to DNA. Specific histone chaperone complexes control the correct deposition of canonical histones and their variants to modulate nucleosome structure and stability and ultimately DNA accessibility. While histone chaperones are highly conserved through evolution, canonical and histone H3 variants have diverged several times in different lineages. Therefore, how histone chaperones contribute to histone variant deposition and chromatin dynamics in plants remains to be understood. We have characterized the Arabidopsis histone chaperone complexes Histone Regulator A (HIRA) and Alpha Thalassemia-mental Retardation X-linked (ATRX) and show that loss of these complexes affects nucleosomal occupancy and genome function. Arabidopsis HIRA and ATRX mutant alleles are viable, but cause severe developmental defects when combined together, suggesting that HIRA and ATRX function in complementary histone H3.3 deposition pathways. Indeed, Arabidopsis ATRX binds H3.3 and ATRX loss-of-function impacts cellular histone H3.3 pools and in consequence modulates the H3.1/H3.3 balance in the cell. At the genome-wide scale, our data indicate that ATRX modifies gene expression through H3.3 deposition at a set of genes characterized both by elevated H3.3 occupancy and high expression levels, altogether emphasizing the role of histone chaperones in regulating chromatin dynamics and fine-tuning genome expression. We are now studying in more detail how coordinated histone deposition contributes to the formation of higher-order chromatin structures and transcriptional regulation. THE USE OF PSEUDOTRYPSIN FOR THE IDENTIFICATION OF PROTEINS FROM BARLEY NUCLEI Zdenek Perutka 1, René Lenobel 1, Beáta Petrovská 2, Hana Jeeábková 2, Jan Vrána 2, Jaroslav Doležel 2, Marek Šebela 1 1- Faculty of Science, Palacký University, Olomouc, Czech Republic 2- Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czech Republic marek.sebela@upol.cz Poster WG2.12 Trypsin is a protease of choice for protein digestion in proteomics. It is well suited for this purpose because of the characteristic cleavage specificity, which involves the peptide bonds at the carboxyl side of arginine or lysine residues. The most typical active forms are the single-chain beta-trypsin and the two-chain alpha-trypsin, which is produced by a limited autolysis of beta-trypsin. An additional intra-chain split between a lysine and arginine residue leads to pseudotrypsin (psi-trypsin, PST). PST was isolated from an autolyzate of TLCK (N-alpha-tosyl-L-lysinylchloromethylketone)- treated trypsin by ion-exchange chromatography following a modification of the original protocol (Smith and Shaw, 1969). Active fractions were pooled, dialyzed against 0.1% (v/v) formic acid, concentrated by ultrafiltration and stored at -80 C. Prior to the digestion of a protein sample, the enzyme was reconstituted in ammonium bicarbonate buffer. A relative quantification procedure based on 18O isotope incorporation during the proteolysis was used to compare the digestion performance of PST and trypsin. PST cleaves predominantly at the characteristic trypsin cleavage sites (Dycka et al., 2015). But in a comparison with common tryptic digestion, non-specific cleavages occur more frequently (mostly after the aromatic residues of tyrosine and phenylalanine) and more missed cleavages are generated. Although the abundance of individual peptides produced by PST differed from the 18O-labeled tryptic standard, the overall digestion performance was comparable (80 %). PST has successfully been applied to identify proteins from barley cell nuclei collected in different cell cycle phases. As a result, unique identifications were achieved to complement parallel trypsin-based data. Smith, R. L. and Shaw, E. (1969) Pseudotrypsin. A modified bovine trypsin produced by limited autodigestion. J. Biol. Chem. 244, Dycka, F.; Franc, V.; Frycák, P; Raus, M.; Rehulka, P.; Lenobel, R.; Allmaier, G.; Marchetti- Deschmann, M. and Šebela, M. (2015) Evaluation of pseudotrypsin cleavage specificity towards proteins by MALDI-TOF mass spectrometry. Protein Pept. Lett. 22,

48 Poster WG2.13 EXPLORING CHROMATIN MOBILITY IN PLANT NUCLEI WITH DRAMATICALLY DISTINCT CHROMATIN ARCHITECTURE AND HETEROCHROMATIN CONDENSATION STATUS. Gianluca Teano, Imen Mestiri, Clara Bourbousse, Chris Bowler, Celia Baroux and Fredy Barneche Institut de Biologie de l Ecole Normale Supérieure CNRS UMR rue d Ulm Paris Cedex 05 France teano@biologie.ens.fr Plants have the remarkable ability to sense and use light conditions as a source of information to adapt their development and physiology accordingly to their environment. For example, the first perception of light by young plantlets induces radical changes with fast molecular reprogramming launching growth and photosynthetic activity. During de-etiolation, cotyledon photomorphogenesis is accompanied by massive rearrangements of heterochromatin organization. More specifically, heterochromatin is mostly aggregated in 8-10 well-defined chromocenters in light-grown cotyledon nuclei, whilst in etiolated cotyledon heterochromatin is more relaxed in the nucleoplasm. Accordingly, exposure of etiolated seedlings to light triggers the condensation of heterochromatic domains within neo-formed chromocenters in cotyledon cell nuclei. This phenomenology has recently led to the identification of histone H1.3 as a key molecular player in triggering light-induced chromatin dynamics (unpublished data). Linker histones are conserved structural components of eukaryotic chromatin that contribute to higherorder chromatin organization by restricting DNA accessibility. Moreover, preliminary results showed that cotyledon chromatin mobility decreases during the first 24h when dark-grown seedlings are exposed to light. More precisely, H2B-RFP signals display a faster recovery rate after Photobleaching (unpublished data), in a coincidental time frame with chromocenters formation. Benefiting from a Short Term Scientific Mission in the laboratory of Dr Baroux at the University of Zürich, and the availability of newly established reporter lines, I will learn how to perform FRAP analyses on light and dark grown cotyledons to further understand the role of the key photomorphogenic regulators and the histone H1.3 variant in defining chromatin mobility properties. EPIGENETIC MODULATION OF RECOMBINANT PROTEIN PRODUCTION IN PLANT CELL CULTURES Plant Cell Biology Laboratory, Instituo de Tecnologia Quimica e Biologica Antonio Xavier, ITQB NOVA, Oeiras, Portugal Rita B. Santos, Ana Sofia Pires, Rita Abranches ritaa@itqb.unl.pt Poster WG3.1 Plant cell cultures are an attractive platform for the production of recombinant proteins. Contrasting to microbial systems, these cells are able to carry out complex protein post translational modifications, but with a much lower production cost than mammalian cells. A major drawback, hindering the establishment of plant cell suspensions as an industrial platform, is the low product yield obtained thus far. Histone acetylation is associated with increased transcription levels, therefore it is expected that the use of histone deacetylase inhibitors would result in an increase in mrna and protein levels. Here, this hypothesis was tested by adding histone deacetylase inhibitors, suberanilohydroxamic acid (SAHA) and trichostatin A (TSA), to a cell line of the model legume Medicago truncatula expressing a recombinant human protein. Histone deacetylase inhibition and histone H3 acetylation levels were studied, and the effect of SAHA and TSA on gene expression and recombinant protein levels was assessed by digital PCR. SAHA or TSA addition inhibited histone deacetylase activity resulting in increased histone H3 acetylation. Higher levels of transgene expression and accumulation of the associated protein were observed. This is the first report describing histone deacetylase inhibitors as inducers of recombinant protein expression in plant cell suspensions as well as the use of digital PCR in these biological systems. This study paves the way for employing epigenetic strategies to improve the final yields of recombinant proteins produced by plant cell cultures. Santos, R.B., Pires, A.S. and Abranches, R. (2017). Addition of a histone deacetylase inhibitor increases recombinant protein expression in Medicago truncatula cell cultures. Scientific Reports 7:

49 Poster WG3.2 NEW BREEDING EFFORTS FOR CLIMATE SMART OIL CROPS Sandra Cvejic, Siniša Jocic, Dragana Miladinovic, Ana Marjanovic Jeromela, Milan Jockovic, Aleksandra Dimitrijevic, Sreten Terzic, Boško Dedic, Vladimir Miklic Institute of Field and Vegetable Crops, Novi Sad, Serbia The total production of oil crops has strongly increased over the past 30 years due to a steadily growing demand in food, feed and non-food uses (e.g. biofuel) of vegetable oils and their by-products. To cope with the impact of climate change, current breeding efforts worldwide are focused on sustainable production and higher oil yield per unit area of land with a view to increase tolerance to biotic and abiotic stress. The Institute of Field and Vegetable Crops (IFVCNS), from Novi Sad, Serbia has long tradition in breeding and production of major oil crops, such as sunflower and rapeseed. In the light of climate changes sunflower is one of the higher adaptation crops due to deep roots prevent erosion and allow drought and other unsuitable conditions to be survived. Therefore, breeding for biotic and abiotic stress tolerance proved to be the most economic and environmental friendly method. Breeding strategies at IFVCNS related to rapeseed are based upon the basic research of seed yield components and seed yield and quality. However, there is a need to develop new varieties which are more efficient in exploiting water, energy, and fertilizer to improve and increase its adaption capability under different environmental conditions and get improved and sustainable yields. Beside sunflower and rapeseed numerous other plant species are also regarded as a possible oil source and various adaptability potentials, such as castor oil plant, safflower, flax, mustard, false flax, sesame, caper spurge, mary thistle and oil pumpkin. This study was supported by Ministry of Education, Science and Technological Development of Republic of Serbia, project TR31025, Provincial Secretariat for Higher Education and Science of Vojvodina, project / , and COST Action CA Jocic, S., Miladinovic, D., Kaya, Y. (2015). Breeding and genetics of sunflower. In: Martinez Force, E., Turgut Dunford, N., Salas, J.J. (eds.), Sunflower: Chemistry, Production, Processing and Utilization, AOCS Press, Urbana, Illinois, USA, 710, Marjanovic Jeromela, A., Terzic, S., Zoric, M., Marinkovic, R., Atlagic, J., Mitrovic, P., Milovac, Ž. (2011). Evaluation of seed and oil yield stability in NS rapeseed cultivars (Brassica napus L.). Ratar. Povrt., 48: DISSECTION OF GENOMIC ARCHITECTURE OF COMPLEX TRAITS AND THEIR PHENOTYPIC PLASTICITY IN TETRAPLOID WHEAT UNDER DROUGHT STRESS Andrii Fathiukha 1, Mathieu Deblieck 2, Lianne Merchuk 3, Zvi Peleg 3, Frank Ordon 2, Yehoshua Saranga 3, Abraham Korol 1, Tzion Fahima 1, Tamar Krugman 1 1- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 31905, Israel. 2- The Robert H. Smith Institute of Plant Science and Genetics in Agriculture, the Hebrew University of Jerusalem, Rehovot 76100, Israel. 3- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, Quedlinburg, Germany tkrugman@univ.haifa.ac.il Poster WG3.3 Phenotypic plasticity is considered one of the major means by which plants adapt to environmental stresses. Adaptive to drought acquired by crop wild relatives can be used for crop improvement. Wild emmer wheat (WEW), Triticum dicoccoides, the progenitor of domesticated wheat, is an important source for wheat improvement. We used high density genetic map derived from T. durum (cv. Langdon) crossed with WEW (G18-16) for QTL mapping of 17 complex traits, including yield, morphology, phenology, biomass and four physiological traits associated with drought response, measured in two water regimes. Residuals of regression between values of traits in control and stress conditions were used as derivative traits for QTL mapping of plasticity in response to drought stress. A total of 33 out of 78 QTLs were identified with plasticity effect on at least one trait. Five QTLs were identified for plasticity traits only, and for nine QTLs we identified effects on plasticity traits without significant effects on the corresponding initial traits. Twelve QTLs affected plastic-yield related traits. The QTL7B.1, with WEW favorable allele, had major plastic effects on yield related traits and phenology. Based on WEW sequence (1) we suggest Vrn-B3 as candidate gene for QTL7B.1. Our results shed light on the genetic architecture of wheat plasticity in response to water stress and confirmed the importance of taking into account variation of phenology in the genetic analysis of plant adaptation. Genetic diversity of WEW allows us to identify new QTLs that can be used for improving drought tolerance of wheat cultivars

50 Poster WG3.4 PLANT CELL WALL INTEGRITY MAINTENANCE AND IMMUNE SIGNALING COOPERATE TO CONTROL STRESS RESPONSES IN Arabidopsis thaliana Timo Engelsdorf 1, Nora Gigli-Bisceglia 1, Manikandan Veerabagu 1, Joseph F. McKenna 2, Lauri Vaahtera 1, Frauke Augstein 1, Dieuwertje Van der Does 3, Cyril Zipfel 3 and Thorsten Hamann 1 1- Department of Biology, Høgskoleringen 5, Realfagbygget, Norwegian University of Science and Technology, 7491 Trondheim, Norway. 2- Department of Biology, S209A Sinclair, Gypsy Lane, Oxford Brookes University, Oxford, OX3 0BP, UK. 3- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK. Thorsten.hamann@ntnu.no The structure and composition of plant cell walls are modified to accommodate the needs of the cell and in response to environmental stimuli. Growth, development, and defense may demand potentially conflicting functional cell wall requirements, and thus modifications of the cell wall are tightly controlled in an adaptive manner. These modifications are mediated by a dedicated cell wall integrity (CWI) maintenance mechanism. Currently, the mode of action of this maintenance system is understood poorly and it is unclear how its activity is coordinated with established plant immune signaling. We investigated both the responses to cell wall damage (CWD) that compromise CWI and the underlying mechanisms in Arabidopsis thaliana. Inhibitor- and enzymetriggered CWD induced similar, turgor-sensitive stress responses. Genetic analysis showed that the receptor-like kinase (RLK) FEI2 and the plasma membrane-localized mechano-sensitive Ca2+- channel MCA1 function downstream of the RLK THE1 in CWD perception. Phenotypic clustering with 27 genotypes identified a core group of RLKs and ion channels required for activation of CWD responses. In contrast, the responses were repressed by pattern-triggered immunity (PTI) signaling components including the receptors for plant elicitor peptides (AtPeps) PEPR1 and PEPR2 (PEPR1/2). Application of AtPep1 and AtPep3 repressed CWD-induced phytohormone accumulation in a concentration dependent manner. CWD induced the expression of both PROPEP1 and PROPEP3 as well as the release of a PROPEP3 fusion protein into the growth medium. These results suggest that AtPep-mediated signaling suppresses CWD-induced defense responses. If key PTI signaling elements acting downstream of PEPR1/2 are dysfunctional, suppression of CWD-induced responses is alleviated, thus compensating for the impairment. ELUCIDATING THE ROLE OF A BROMOIDOMAIN PROTEIN ENABLING VIROID AND SATELLITE VIRUS INFECTIVITY. Katsarou K. 2, Iliopoulou M. 1, Michalopoulou V. 1, Bardani E.. 1, Kalantidis K. 1,2 1- Dept. of Biology, University of Crete, Heraklion, Greece 2- Institute of Molecular Biology and Biotechnology,- FoRTH, Heraklion, Greece kriton@imbb.forth.gr Poster WG3.5 Viroids are naked, circular single stranded lncrna pathogens that range in size from 246 to 467nt, causing plant diseases of significant economic importance. They are considered non- protein coding and do not require a helper virus for infection. Their genomic non-protein coding RNA carries all the information for host specificity, replication, systemic spreading, sub-cellular localization and interaction with host factors. All their biological cycle, infection, replication, intra- and intercellular movement, overcoming host defense and new infection, result from interactions with host factors. Viroids of the Pospi-clade replicate in the nucleus and their nuclear import of viroid RNA is presumably mediated by host factors. Although such host factors have not been unequivocally characterized todate, VIRP1 could function as a sub-cellular transporter of this group of viroids as has been shown for the CMV-satRNA, a cellular pathogen that shares important similarities with viroids. This protein was shown to be a necessary factor for viroid and CMVsat replication (Chaturvedi et al., 2014; Kalantidis et al., 2007). VIRP1 belongs to bromodomain proteins, found in transcription complexes, where they perform scaffolding functions maintaining close vicinity to chromatin; they have been implicated in viral pathology before holding important roles in some human viruses (HIV, Epstein-Barr and more). We have produced and tested VIRP1-overexpressing and RNAi transgenic lines and showed that KD plants cannot be infected by viroids and CMV-sat. In order to functionally characterize VIRP1 we are currently generating CRISPR mutants. In addition, we have constructed VIRP mutants and successfully tested VIRP1:GFP and VIRP1:FLAG fusions. Chaturvedi, S., Kalantidis, K., and Rao, A.L. (2014). A bromodomain-containing host protein mediates the nuclear importation of a satellite RNA of Cucumber mosaic virus. J Virol 88, Kalantidis, K., Denti, M.A., Tzortzakaki, S., Marinou, E., Tabler, M., and Tsagris, M. (2007). Virp1 is a host protein with a major role in Potato spindle tuber viroid infection in Nicotiana plants. J Virol 81, v 98 99

51 Poster WG3.6 THE CHARACTERIZATION OF EPIGENETIC REGULATORS DURING SEED DEVELOPMENT AND ABIOTIC STRESS- RESPONSE IN DIFFERENT BARLEY CULTIVARS Aliki Kapazoglou 1#, Vicky Drossou 1, Dimitra Papaefthimiou 1, Anagnostis Argiriou 1, Athanasios Tsaftaris 1,2,3 1- Institute of Applied Biosciences (INAB), CERTH, Thermi-Thessaloniki, GR , Greece #current address: Institute of Olive tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (Demeter), Lykovrysi, Athens, GR-14123, Greece 2- Department of Genetics and Plant Breeding, Aristotle University of Thessaloniki, Thessaloniki, GR-54124, Greece 3- Perrotis College, American Farm School, Thessaloniki, Greece The regulation of various plant processes such as vegetative, flower and seed development and the response to environmental changes is often mediated by epigenetic mechanisms like DNA methylation, histone modifications and the action of small RNAs which modulate chromatin structure and profoundly affect gene expression. To understand the epigenetic molecular mechanisms that regulate the development of barley an agronomically important cereal in Europe and worldwide, a series of barley genes encoding chromatin modifiers such as histone methyltransferases and demethylases, histone acetylases and histone deacetylases and DNA demethylases, was characterized and its expression examined at different stages of seed development, in response to stress related hormones and in response to drought. Differential expression was evidenced for the epigenetic regulators at different developmental stages and under the effect of different hormonal treatments. In addition, a barley histone demethylase homologue (HvPKDM7) and a DNA glycosylase (DME) were found to be induced under conditions of drought stress in a cultivar-dependent manner. The knowledge obtained from this research could be utilized for the generation of molecular markers for selecting suitable genotypes during Triticeae breeding programmes aiming to the development of improved Triticeae varieties enhanced in nutritional seed content, and in the tolernace of the plant to stresses and changing climatic conditions. A META-ANALYSIS OF THE TOBACCO POLLEN TRANSCRIPTOME. ACTIVELY TRANSLATED AND STORED NUCLEAR GENES DURING POLLEN DEVELOPMENT Christos Michailidis 1, Said Hafidh 1, David Potršil 2,3, Katarína Kulichová 1, Karel Müller 4, Jan Fíla 1, Jana Feciková 1, Zbynrk Zdráhal 2,3, David Honys 1 1- Laboratory of Pollen Biology, Institute of Experimental Botany, ASCR, v.v.i., Rozvojová 263, Prague 6, Czech Republic 2- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, Czech Republic 3- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, Czech Republic 4- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, ASCR, v.v.i., Rozvojová 263, Prague 6, Czech Republic christos@ueb.cas.cz Poster WG3.7 The male gametophyte, a highly organized haploid organ, offers a unique chance to analyze development and differentiation of a single haploid cell. Transcriptomic studies clearly showed that male gametophyte development is under control of two subsequent developmental programs, early and late, accompanied by stage-specific gene expression patterns (1, 2). A number of pollen mrnas were shown to be bound to pollen stored ribonucleoprotein particles. Some of the stored messages are translationally silenced at earlier stages of development and activated during the maturation processes of the pollen grain. Here, we present a meta-analysis of the transcriptome of stored and translated nuclear genes throughout tobacco pollen development (uninucleate microspores, early bicellular pollen, late bicellular pollen, mature pollen and in two stages of progamic phase (in vitro cultivated pollen tubes for 4h and 24h). In an effort to understand the nature and diversity of transcripts associated with actively translating or stored fractions, we applied tobacco microarray technology (Imaxio) and performed the comparative microarray analysis. Arabidopsis thaliana nuclear gene families filtered for associated function inferred via experimental evidence alone were identified in AmiGO 2 (3, 4) and used to screen the transcriptomic data. As part of our analysis we identified that histones share early expression profile being predominantly associated with actively translated transcripts but some histone-modifying gene families show active transcription late in the progamic phase. DNA binding transcription factors have a more diverse pattern of active transcription with some stress related genes actively expressed late in the progamic phase

52 Poster WG3.8 Poster WG3.9 COMPARATIVE PHENOTYPIC AND METABOLIC ANALYSIS OF HELIANTHUS SPECIES FOR IMPROVED STRESS RESILIENCE Dragana Miladinovic, Aleksandra Dimitrijevic, Sandra Cvejic, Siniša Jocic, Boško Dedic, Milan Jockovic, Ana Marjanovic Jeromela Institute of Field and Vegetable Crops, Maksima Gorkog 30, Novi Sad, Serbia The species of the genus Helianthus have very broad spectrum of life forms since they occupy diverse habitats. Cosmopolitan distribution of these species could be explained by a number of anatomical and physiological mechanisms that create the basis for survival of the plants in a wide variety of habitats. At the Institute of Field and Vegetable Crops (IFVCNS), Novi Sad, there is one of the largest collection of annual and perennial sunflower species, interspecific hybrids, sunflower varieties, lines and hybrids worldwide ( This collection has been actively used in breeding as a source of disease resistance and abiotic stress resistance genes. Within the framework of ongoing projects, we have started to perform comparative phenotypic and metabolic analysis of genotypes chosen from IFVCNS collection in order to identify morphological and metabolic parameters of various plant organs that could be useful tools for detection of genotypes tolerant to different environmental stresses. This will be further complemented by molecular analyses for identification of QTLs correlated to abiotic and biotic stresses. The final aim of this combined approach to stress resilience study in sunflowers is to identify genotypes with desirable traits that could be further included in sunflower breeding programs and creation of highly productive stress resistant hybrids, as well as to create an ideotype specific for certain agro-ecological conditions. Acknowledgements This study was supported by Ministry of Education, Science and Technological Development of Republic of Serbia, project TR31025, Provincial Secretariat for Higher Education and Science of Vojvodina, project / , and COST Action CA REPRODUCTIVE TRAITS STUDY FOR IMPROVEMENT OF LOCAL VITICULTURE IN ARMENIA Nebish A.A. 1,2, Aroutiounian R.M 1,2 1- Yerevan State University, Department of Genetics and Cytology, 1 Manoogian st., 0025 Yerevan, Armenia 2- Institute of Molecular Biology of NAS RA, Research group of Plant genetics and Immunology, 7 Hasratyan st., 0014, Yerevan, Armenia anita.nebish@gmail.com Armenia is considered as one of the most important centers of grape origin and biodiversity. High sterility of female and male gametophytes as a result of failed meiosis causes the flower bud abscission and consequently the low fruit set in some grapevine cultivars. It depends on origin and genetic characteristics of varieties, gene expression and phenotype development in different environmental conditions. For cytoembryological studies the flowers of 10 local ancient and new bred grapevine varieties were fixed by FAA fixative and treated by using common paraplast-embedding and sectioning techniques combined with double staining by Mayer s hematoxylin and eosin (H&E). Different levels of reproductive cells viability were registered by microscopic observation of flowers sections. The level of pollen variability varied from 72.1% to 97.5% in ancient and from 58.3% to 90.1% in new bred varieties. In the ovaries instead of 4 potential ovules only 1-3 ovules with eight cells of embryo sacs were developed. The ovules viability varied from 32,0% to 62,5% in investigated varieties irrespective of their origin. Obtained results demonstrated an importance of cytoembryological approach for understanding problems regarding fruit set and yield level. Our data are actual for the efficient exploitation of plant genetic resources and breeding new cultivars with improved quality, stable yield and reduced economic and environmental costs (Royo et al., 2015; Aroutiounian et al., 2012). Acknowledgements. This research was partially funded by Research projects of State committee of science at the Ministry of Education and Science of Armenia (Armenian 15T- 1E232 and Armenian German 16GE-042 grants). Royo, C., Carbonell-Bejerano, P., Torres-Pérez, R., Nebish, A., Martínez, O., Rey, M., Aroutiounian, R., Ibáñez, J., Martínez-Zapater, J.M. (2016) Developmental, transcriptome, and genetic alterations associated with parthenocarpy in the grapevine seedless somatic variant Corinto bianco. J. Exp. Bot. 67(1), Aroutiounian, R., Nebish, A., Melyan, G., Margaryan, K. (2015) Phenotypic profiles of Armenian grape cultivars. BIO Web of Conferences 5,

53 Poster WG3.10 Poster WG3.11 FINE ORGANIZATION OF GENOMIC REGIONS TAGGED TO THE 5S rdna LOCUS OF THE BREAD WHEAT 5B CHROMOSOME Ekaterina M. Sergeeva, Andrey B. Shcherban, Irina G. Adonina, Elena A. Salina The Federal Research Center Institute of Cytology and Genetics SB RAS,Novosibirsk, Russia The multigene family encoding the 5S rrna, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rdna has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rrna genes remains unclear. This is despite the recent progress made in wheat genomic sequencing. Using pyrosequencing of BAC clones, in this work we studied the organization of two distinct 5S rdna-tagged regions of the 5BS chromosome of bread wheat. Three BAC-clones containing 5S rdna were identified in the 5BS chromosomespecific BAC- library of Triticum aestivum. Using the results of pyrosequencing and assembling, we obtained six 5S rdna- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rdna sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. Both regions are characterized by the presence of approximately copies of 5S rdna, however, they are completely different in their structural organization. The first region contained highly diverged short-type 5S rdna units that were disrupted by multiple insertions of transposable elements. The second region contained the more conserved long-type 5S rdna, organized as a single tandem array. FISH using probes specific to both 5S rdna unit types showed differences in the distribution and intensity of signals on the chromosomes of polyploid wheat species and their diploid progenitors. Conclusion: A detailed structural organization of two closely located 5S rdnatagged genomic regions on the 5BS chromosome of bread wheat has been established. These two regions differ in the organization of both 5S rdna and the neighboring sequences comprised of transposable elements, implying different modes of evolution for these regions. NOVEL APPROACHES TO ANALYSING RIBOSOMAL RNA MULTIGENE LOCI IN BARLEY Toegelova, H. 1, Mascher, M. 2, Macas, J. 3, Beseda, T. 1, Tulpova, Z. 1, Tanskanen, J. 4, Schulman, A.H. 4, Dolezel, J. 1, Stein, N. 2, Simkova, H Institute of Experimental Botany, Slechtitelu 31, CZ Olomouc, Czech Republic 2- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Corrensstr. 3, D Stadt Seeland, Germany 3- Institute of Plant Molecular Biology, Branisovska 31, CZ Ceske Budejovice, Czech Republic 4- LUKE Natural Resources Institute Finland & Institute of Biotechnology, University of Helsinki, Latokartanonkaari 9, FI-00790, Helsinki, Finland simkovah@ueb.cas.cz Ribosomal RNA gene loci pose an indispensable part of both prokaryotic and eukaryotic genomes. In eukaryotes, they are associated with nucleolus, the largest functional domain of the nucleus and the site of ribosomal biogenesis. They are mostly organized as long head-to- tail tandem arrays spanning several hundred kilobases to multiple megabases, which precludes their complete assembling from NGS data and impedes characterization of particular loci. In our study, we identified and analysed 26S-5.8S-18S rrna multigene loci in barley genome by Bionano genome (BNG) mapping, a technology that visualizes short sequence motives along DNA molecules of 150 kb to 1 Mb. 45S rdnas appear as labelled simple or compound repeats in Bionano genome maps created using Nt.BspQI nicking enzyme. They can be recognized in the maps according to their characteristic label pattern. Ribosomal DNA units in cultivated barley (Hordeum vulgare) have a size of ~9 kb and are observed as both simple and two-label compound repeats. Only the compound variant, featured by additional BspQI site, was identified in genome maps of wild barley (H. spontaneum). Combination of BNG mapping with other approaches such as Hi-C on barley mitotic chromosomes and long-read nanopore sequencing facilitated positioning and characterization of both major and minor 45S rdna loci in barley genome, which built the basis for analysis of their transcription activity as well as interactions in 3D nucleus

54 Poster WG3.12 Poster WG3.13 SEEDLINGS GROWTH AND TRANSCRIPTIONAL RESPONSES TO SALT AND DROUGHT STRESS OF MEDICAGO SATIVA L, MEDICAGO ARBOREA L. AND THEIR HYBRID (ALBOREA) Eleni Tani 1 and Eleni Abraham 2 1- Department of Crop Science, Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, IeraOdos 75, Athens, Greece 2- Faculty of Agriculture, Forestry and Natural Environment, School of Forestry, Aristotle University of Thessaloniki eabraham@for.auth.gr Salinity and drought are major limiting factors of crops productivity worldwide. Medicago sativa L. is an important fodder crop with high nutritive value, broadly cultivated in different environments and is a moderately salt and drought tolerant species. On the other hand, Medicago arborea L. that is considered a stress tolerant species could be an important genetic resource for the improvement of tolerance of M. Sativa to both stresses. The aim of the present study was to evaluate the seedling response of M. sativa, M. arborea and their hybrid (Alborea) to salt and drought stress. Three salt stress treatments (50 mm, and mmnacl gradual acclimatization), two salt shock (100 and 150 mmnacl) and water deficit treatment were applied to seedlings. Growth rates and transcriptional profiles of NHX1, RCI2A, P5CS1, SMIKK, ZGF, AP2/EREBP genes were evaluated. M. sativa and M. arborea performed similarly good under stress. Alborea exceeded in productivity compared to its parents under normal conditions. Nevertheless, Alborea was extremely sensitive to stresses. M. sativa and M. arborea seem to regulate different components of tolerance mechanisms. Knowledge of the different parental mechanisms of salt and drought tolerance could play an important role into incorporating both mechanisms in their hybrid. RESPONSE OF SUGAR BEET GENOTYPES TO IN VITRO INDUCED WATER DEFICIT Ksenija Taški Ajdukovic, Nevena Nagl, Živko Curcic, Mihajlo Criic, Nada Grahovac Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia ksenija.ajdukovic@ifvcns.ns.ac.rs Sugar beet is one of the most important industrial crops. In many areas of sugar beet production, the water deficit during the summer significantly limits the root yield and the sugar content. Since breeding for drought tolerance is economically the most viable solution for overcoming this problem, it is necessary to understand the reaction of sugar beet genotypes to the conditions of water deficit. As part of an extensive study of sugar beet reaction to drought stress, this research was conducted with the aim to detect changes in growth parameters, proline content and the expression of candidate genes during the in vitro induced water deficit. Sugar beet genotypes, selected for various responses to reduced water supply, were micropropagated on media with 0%, 3% and 5% polyethylene glycol (PEG) for 28 days. The number of axillary shoots was reduced, while the dry matter content increased with the severity of the PEG concentration. No differences were detected between shoot weight of controls and treatments in any genotype. Proline content in some genotypes did not change with increase of PEG concentration, while in others PEG treatments caused increase in proline content. The selected candidate genes differed in relative gene expression among genotypes and applied PEG treatments. The results showed that investigated morphological, physiological and genetic parameters have potential to be used in the assessment of sugar beet tolerance to water deficit

55 Poster WG3.14 ANALYSIS OF PLANT GENOME STRUCTURE USING MOLECULAR CYTOGENETICS TOOLS Ahmet L. Tek Department of Agricultural Genetic Engineering, Ayhan Tahenk Faculty of Agricultural Sciences and Technologies, NiTde Ömer Halisdemir University, 51240, NiTde, Turkey Eukaryotic genomes are confined within a small compartment called nucleus. Traditionally nucleus harbors heavily stained nucleoprotein complex known as heterochromatin (Franz and de Jong, 2011). Plant centromeres are known to contain highly divergent DNA and diverse protein sequences (Houben and Schubert, 2003). We have characterized the DNA and protein components of functional centromeres in several legume species (Iwata et al., 2013; Tek et al., 2010; 2011; 2014). In our current work, we aim to functionally characterize the heterochromatin region of centromeres in sainfoin, Onobrychis viciifolia, first by cloning the centromeric histone H3 (CenH3), subsequently, developing a polyclonal antibody to identify the centromeric DNA sequences by chromatin immunoprecipitation technique. Mapping the centromeric DNA and CENH3 protein on nuclei and metaphase chromosomes might provide a partial information on the global organization of nuclear domains. In addition, we will share our preliminary studies on meiosis and ribosomal genes in plants. As a member of COST Action CA16212 and in line with the consortium, we eagerly plan to broaden our work to better understand the organization and dynamic features of centromeric and noncentromeric DNA sequences in agriculturally important and model legumes. Houben, A., and Schubert, I. (2003). DNA and proteins of plant centromeres. Current Opinion in Plant Biology 6, Iwata, A., Tek, A.L., Abernathy, B., Schmutz, J., Thareau, V., Murata, M., Geffroy, V., Nagaki, K., and Jackson, S.A. (2013). Identification and characterization of functional centromeres of the common bean. Plant J 76, Fransz, P., and de Jong, H. (2011). From nucleosome to chromosome: a dynamic organization of genetic information. Plant J 66, Tek, A.L., Kashihara, K., Murata, M., and Nagaki, K. (2010). Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon. Chromosome Res 18, Tek, A.L., Kashihara, K., Murata, M., and Nagaki, K. (2011). Functional centromeres in Astragalus sinicus include a compact centromere-specific histone H3 and a 20-bp tandem repeat. Chromosome Res 19, Tek, A.L., Kashihara, K., Murata, M., and Nagaki, K. (2014). Identification of the centromere-specific histone H3 variant in Lotus japonicus. Gene 538, Poster WG3.15 NUCLEAR CHANGES ASSOCIATED WITH STRESS INDUCED MICROSPORE EMBRYOGENESIS M. P. Vallés 1, E. Dubas 2, I. Zur 2, R. A. Sánchez-Díaz 1,2, A. M. Castillo 1 1- Aula Dei Experimental Station, The Council for Scientific Research (EEAD- CSIC), Avda Montañana 1005, Zaragoza, Spain 2- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, Kraków, Poland 3- Present address: Genetic Resources and Biotechnology Management, INIA- DRGB, Av. La Molina 1981, Lima, Peru. valles@eead.csic.es Doubled haploid are a valuable tool in both plant breeding and cell and molecular biology. Microspore embryogenesis (ME) is one of the most efficient methods for doubled haploid plant production. In ME, microspores triggered by stress deviate from the gamethopytic towards the sporophytic developmental pathway under optimal in vitro culture conditions. Sugar starvation and osmotic stress have been shown to efficiently induce ME in barley and wheat. Some of the first visible intracellular dynamic changes associated with stress-induced ME are the movement of the nucleus towards the cell center and the preprophase band (PPB) formation. The presence of PPB precedes the first symmetric mitotic division, which leads to a multicellular embryo-like structure formation. These morphological events are accompanied by the activation of nucleus cellular component genes, including those involved in DNA replication, chromatin remodeling and RNA processing. Particularly, n-butanol which as well as the histone deacetylase inhibitor (Trichostatin A, TSA) which modifies have been reported to improve ME induction (Soriano et al., 2008; Castillo et al., 2014; Li et al., 2014). The main interest of our work is the identification and characterization of the molecular mechanism, the targets genes and nucleus dynamics associated with ME induction by TSA action. Castillo, A. M., Nielsen, N. H., Jensen, A., Vallés, M. P. (2014). Effects of n-butanol on barley microspore embryogenesis. Plant Cell, Tiss Org Cult 117(3), Li, H., Soriano, M., Cordewener, J., Muiño, J. M., Riksen, T., Fukuoka, H., Boutilier, K. (2014). The histone deacetylase inhibitor trichostatin a promotes totipotency in the male gametophyte. The Plant Cell 26(1), Soriano, M., Cistué, L., Castillo, A.M. (2008) Enhanced induction of microspore embryogenesis after n-butanol treatment in wheat (Triticum aestivum L.) anther culture. Plant Cell Rep 27,

56 Abstract WG2.16 No Poster submitted Poster WG4.1 Histone H2A (de)ubiquitination affects the function of the circadian clock in Arabidopsis thaliana Anita Hajdu 1, Ferenc Nagy 1, László Kozma-Bognár 1,2 1- Institute of Plant Biology, Biological Research Center, Szeged, H-6726, Hungary 2- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, Szeged, H-6726, Hungary In order to identify novel components of the circadian system in Arabidopsis thaliana, we carried out a large-scale forward genetic screen. Several mutants, displaying altered rhythmic expression pattern of the CAB2:LUC reporter gene in continuous light conditions, were isolated. The mutant rs24 (red screen 24) showed about 2 h period shortening under the screening conditions and was selected for further analysis. The mutation affected the expression of several clock-controlled genes in the same manner and the short period phenotype was independent of the light conditions. These findings indicated that the function of the core oscillator was altered in the mutant. In fact, expression of the core clock genes showed the expected short period phenotype, but the level of their expression was not affected significantly. This suggests that RS24 does not affect transcription of clock components directly. Consistent with the basic circadian dysfunction, rs24 showed early flowering phenotype in short day conditions. rs24 mutants produce long hypocotyls in red light, suggesting a positive role for RS24 in phytochrome-mediated light responses. Genetic mapping followed by transgenic complementation showed that the RS24 gene encodes an ubiquitin protease, known as UBP12. This enzyme has been show to influence the ubiquitination state of histone H2A and via the modulation of the activity of the Polycomb group protein complex, it affects heterochromatic gene repression (Derkacheva et al., 2016). Although we have not discovered the direct molecular link yet, our results underline the important function of chromatin remodeling in the regulation of the plant circadian oscillator. Derkacheva, M., Liu, S., Figueiredo, D.D., Gentry, M., Mozgova, I., Nanni, P., Tang, M., Mannervik, M., Köhler, C., and Hennig, L. (2016) H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system. Nat Plants. 2: doi: /nplants HPC AND GPGPU FOR LARGE-SCALE IMAGE PROCESSING Cédric Charière Fiedler, Rémy Malgouyres LIMOS Campus Universitaire des Cézeaux 1 rue de la Chebarde TSA CS AUBIERE CEDEX - FRANCE chariere@isima.fr The size of data generated by the sensors increases in correlation with the improvement of their resolution. In the big data era, the memory and the time required to process one large-scale image can be too high to be computed on a single processor. The Graphical Processing Units are, by design, efficient to apply the same process to a large volume of data. The current OpenCL abstraction: Sycl1.2.1, provides a solution to write, in a single-source style, a code for heterogeneous processors using the complete C++ syntax. We study opportunities given by the Sycl technology and High-Performance Computing methods, to process large two and three-dimensional images with generic algorithms. The goal of this work is to develop an abstract algorithmic structure dedicated to each step of data processing: fetching, tiling, computing, merging and loading. This structure will take into consideration the performance requirements, such as the data alignment and synchronization of the image structure between the computing devices. The high resolution images requires a specific attention to be processed. The current open technologies, such as ImageJ, are not designed to compute them: because of their energy consumption, the memory requirement and/or the use or a single CPU. Our approach is particularly relevant for the nanoscale optical microscopy. We are proposing a high throughput processing technique tiling the large-scale images and distributing them into a GPU cluster, in high-performing way. Keywords: GPGPU, HPC, large-scale image processing, distributed computing Khronos OpenCL Working Group SYCL subgroup. (2017). SYCL Specification A. Vilches, R. Reyes. (2016). SyclParallelSTL: A Parallel STL library for Heterogeneous Systems J.J Dongarra, A. J. van der Steen. (2012). High-performance computing systems: Status and outlook Marc Baboulin, Joel Falcou, Ian Masliah. (2014). Towards an automatic generation of dense linear algebra solvers on parallel architectures Gonzalo P. Rodrigo. (2017). HPC scheduling in a brave new world Murray I. Cole. (1990). Algorithmic Skeletons: Structured Management of Parallel Computation U. Dastgeer. (2011). Skeleton Programming for Heterogeneous GPU-based Systems

57 Poster WG4.2 AuBI PLATFORM FOR BIOLOGISTS AND BIOINFORMATICIANS AT UCA MESOCENTRE Nadia Goué, David Grimbichler and Antoine Mahul AuBi, Platform Auvergne Bioinformatics, Clermont Auvergne Mésocentre, Clermont Auvergne University, 7, avenue Blaise Pascal, CS 60026, Aubière cedex, France The Mesocentre as part of Clermont Auvergne University (UCA) is delivering services in sciences data computing (HPC, VM, ) and short-term storage through a network of technology core facilities. These offers are done to assist multi-disciplinary scientists in their computing projects. Hosted by the Mesocentre, the Auvergne bioinformatics (AuBi) platform is a member of the French Bioinformatics Institute (IFB). AuBi platform aims at sharing expertises and knowledge in large- scale data treatment and analysis by supplying a complete computing environment with hardware and software infrastructures for about 10 research laboratories, for example [1,2,3]. AuBi platform is then involved in various projects belonging to genomics, metagenomics, transcriptomics, metabolomics, epigenetics, genetics, modeling and imaging fields amongst others. Furthermore, we provide support to UCA laboratories and Associates in their effort to maintain and enhance their scripts and pipelines used on our infrastructure. Another aspect of AuBi platform work is to facilitate computing access to non-bioinformatician biologists by the way of a Galaxy server released in the upcoming weeks. We are also organizing training sessions to help our users, either biologists or bioinformaticians to optimize computing resources usage through command line interface and Galaxy environment. 1. Amato P., Joly M., Besaury L. Oudart A., Taib N., Moné A., Deguillaume L., Delort A.M. and Debroas D. (2017). Active microorganisms thrive among extremely diverse communities in cloud water. PLoS ONE 12(8):e Gasc C, Constantin A, Jaziri F, Peyret P: OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture. Database (Oxford) 2017, Parisot N, Peyretaillade E, Dugat-Bony E, Denonfoux J, Mahul A, Peyret P: Probe Design Strategies for Oligonucleotide Microarrays. Methods Mol Biol 2016, 1368:

58 Workshop Attendees Workshop Attendees Mariamawit ASHENAFI SWITZERLAND Eleni ABRAHAM GREECE Nadia FERNANDEZ SPAIN Paul FRANSZ NETHERLAND Rita ABRANCHES PORTUGAL Rafal ARCHACKI POLAND Valérie GAUDIN FRANCE Danny GEELEN BELGIUM Zikrija AVDAGIC BOSNIA AND HERZEGOVINA Fredy BARNECHE FRANCE Céline GONTHIER-GUERET FRANCE Nadia GOUE FRANCE Céclia BAROUX SWITZERLAND Till BEY NETHERLAND Katja GRAUMANN UNITED KINGDOM Stephan GROB SWITZERLAND Marie-Edith CHABOUTE FRANCE Cédric CHARIERE FRANCE Bjoern GRUENING GERMANY Hana JERABKOVA CZECH REPUBLIC Christian CHEVALIER FRANCE Isabelle COLAS UNITED KINGDOM Michel KADLOF POLAND Kriton KALANTIDIS GREECE Nicolas CORRE FRANCE Sandra CVEJIC SERBIA Aliki KAPAZOGLOU GREECE Marta KOBLOWSKA POLAND Nicolas DESFORGES FRANCE Sophie DESSET FRANCE Laszlo KOZMA-BOGNAR HUNGARY Kalyani KRISHNA GERMANY Tristan DUBOS FRANCE Tao DUMUR AUSTRIA Tamar KRUGMAN ISRAEL Thierry LANGIN FRANCE Susan DUNCAN UNITED KINGDOM Martina DVORACKOVA CZECH REPUBLIC David LATRASSE FRANCE Samuel LE GOFF FRANCE David EVANS UNITED KINGDOM Sara FARRONA IRELAND Inna LERMONTOVA GERMANY Chang LIU GERMANY

59 Workshop Attendees Rémy MALGOUYRES FRANCE Jérénmy MEHZOUD FRANCE Workshop Attendees Aline PROBST FRANCE Dimiter PRODANOV BELGIUM Anis MESCHICHI SWEDEN Christos MICHAILIDIS CZECH REPUBLIC Stefanie ROSA-NUNES SWEDEN Elena SALINA RUSSIAN FEDERATION Pawel MIKULSKI UNITED KINGDOM Dragana MILADINOVIC SERBIA Daniel SCHUBERT GERMANY Marek SEBELA CZECH REPUBLIC Ortrun MITTELSTEN SCHEID AUSTRIA Iva MOZGOVA CZECH REPUBLIC Hana SIMKOVA CZECH REPUBLIC Lauriane SIMON SWEDEN Anna NEBISH ARMENIA Mélody NICOLEAU FRANCE Pierre SOURDILLE FRANCE Ioanna STAVRIDOU BELGIUM Samir OMANOVIC BOSNIA AND HERZEGOVINA Giorgio PAPADOPOULOS FRANCE Szymon SWIEZEWSKI POLAND Ksenija TASKI-AJDUKOVIC SERBIA Geraint PARRY UNITED KINGDOM Zofia PARTEKA POLAND Christophe TATOUT FRANCE Guillaume TATTI FRANCE Wyatt PAUL FRANCE Etienne PAUX FRANCE Gianluca TEANO FRANCE Ahmet TEK TURKEY Ales PECINKA CZECH REPUBLIC Zdenek PERTUKA CZECH REPUBLIC Hamann THORSTEN NORWAY Maria Pilar VALLES BRAU SPAIN Ariadna PICART-PICOLO FRANCE Jean-Philippe PICHON FRANCE Emmanuel VANROBAY FRANCE Serena VAROTTO ITALY Frederic PONTVIANNE FRANCE Monica PRADILLO SPAIN Chantal VAURY FRANCE

60 Notes

61 COST_INDEPTH Kickoff Meeting GARNet2018: a plant science showcase University of York September 18-19th 2018 Five Plenary Sessions: > Large Scale Biology > Innovations in Hormone Signaling > Interacting with the environment > Out of Arabidopsis > Novel Cell Imaging > Keynote: Prof Dame Ottoline Leyser > 10 talks from abstracts > 15 Flash presentations 120