Genomic Elements in Health, Disease and Evolution

Transcription

1 Genomic Elements in Health, Disease and Evolution

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3 Kyriacos Felekkis Konstantinos Voskarides Editors Genomic Elements in Health, Disease and Evolution Junk DNA

4 Editors Kyriacos Felekkis Department of Life and Health Sciences and University of Nicosia Medical School University of Nicosia Nicosia, Cyprus Konstantinos Voskarides Department of Biological Sciences Molecular Medicine Research Center University of Cyprus Nicosia, Cyprus ISBN DOI / ISBN (ebook) Library of Congress Control Number: Springer New York Heidelberg Dordrecht London Springer Science+Business Media New York 2015 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper Springer Science+Business Media LLC New York is part of Springer Science+Business Media (

5 Preface Although the term junk DNA was used since the early 1960s, the term s origin was attributed to Susumo Ohno who officially used the term to describe pseudogenes sequences resulted from gene duplication and subsequent mutagenesis events. Since then, the term was widely used to describe any non-coding sequence of the genome. Today, junk DNA refers to any genomic sequence that does not play a functional role in the organism. The use of the term was accompanied by various unanswered questions: Why do we have so much junk DNA in our genome? Do these non-coding sequences have functional significance? The discovery of novel genomic elements in the recent years was a step forward in an attempt to address these issues. It appears that the percentage of the non-functional DNA is being significantly reduced as more and more functions are attributed to those noncoding regions of the genome. Despite the continuous shrinkage of the nonfunctional portion of the genome, it is believed that a significant part of the genome is indeed non-functional. In this book, we attempt to provide a thorough review of various non-coding genomic elements and discuss in depth their role in health, disease and evolution. We begin our exploration with non-coding RNA molecules, mirnas, pirnas, LncRNAs and transposable elements as these moieties dominate the scientific literature in the last 10 years. We proceed with the discussion of copy number variation regions, mini- and micro-satellites, and proximal and distal elements of the genome. The last section of this book focuses on the review of well-known noncoding regions of the genome, introns, centromeres and telomeres, but enriched with newly discovered functions. As the vast amount of data in regard to these elements is attributed to a great degree to the growing technology in the field of biomedicine, the last chapter of this book discusses the latest development in the field of Next Generation Sequence and the potential applications of this technology in the study of non-coding regions of the genome. The original structure of this book was greatly shaped by many conversations with colleagues in Cyprus and abroad. We are indebted to all the authors contributing to this publication for their in-depth review of the subject and their excellent writing. We must also thank all the scientists whose work is included in this book. v

6 vi Preface Special thanks to our respective institutions and colleagues for their support and critical interventions. The driving force of our inspiration is equivocally our students who provide us with the strength and willingness to sit down and write. Last but not least, we are indebted to our families and friends for their continuous support and encouragement. Nicosia, Cyprus Kyriacos Felekkis Konstantinos Voskarides

7 Contents 1 MiRNAs Function and Role in Evolution: Under the View of Genomic Enhancement Phenomena... 1 Konstantinos Voskarides and Kyriacos Felekkis 2 MicroRNAs in Disease Gregory Papagregoriou 3 pirnas-transposon Silencing and Germ Line Development Catherine Demoliou 4 Long Non-coding RNA Monika Gullerova 5 Unveiling Transposable Elements Function to Enrich Knowledge for Human Physiology and Disease Pathogenesis Ioannis S. Vizirianakis, Elsa P. Amanatiadou, and Sotirios S. Tezias 6 Copy Number Variation in Human Health, Disease and Evolution Carolina Sismani, Costas Koufaris, and Konstantinos Voskarides 7 Mini- and Micro-Satellite Markers in Health, Disease and Evolution Vasiliki A. Galani, Sofia Markoula, Leandros Lazaros, Paris Ladias, and Ioannis Georgiou 8 Intron Biology, Focusing on Group II Introns, the Ancestors of Spliceosomal Introns María Dolores Molina-Sánchez, Rafael Nisa-Martínez, Fernando M. García-Rodriguez, Francisco Martínez-Abarca, and Nicolás Toro 9 Centromeres in Health, Disease and Evolution Thian Thian Beh and Paul Kalitsis vii

8 viii Contents 10 Structure and Functions of Telomeres in Organismal Homeostasis and Disease Penelope Kroustallaki and Sarantis Gagos 11 Proximal Regulatory Elements with Emphasis on CpG Rich Regions Pavlos Fanis 12 Genomic Analysis Through High-Throughput Sequencing Michalis Hadjithomas Index

9 Contributors Elsa P. Amanatiadou, M.Sc. Laboratory of Pharmacology, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece Thian Thian Beh, B.Sc. (Hons.) Murdoch Childrens Research Institute, Royal Children s Hospital, Parkville, VIC, Australia Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia Catherine Demoliou, Ph.D. Life and Health Sciences Department, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus Pavlos Fanis, B.Sc., Ph.D. Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus Kyriacos Felekkis, B.Sc., Ph.D. Department of Life and Health Sciences, University of Nicosia Medical School, University of Nicosia, Nicosia, Cyprus Sarantis Gagos, Ph.D. Department of Experimental Medicine and Translational Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece Vasiliki A. Galani, Ph.D. Department of Anatomy Histology Embryology, University of Ioannina, Ioannina, Epirus, Greece Fernando M. García-Rodriguez, Ph.D. Grupo de Ecología Genética, Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín/ Consejo Superior de Investigaciones Científicas, Granada, Spain Ioannis Georgiou, Ph.D. Division of Reproductive Genetics, Department of Obstetrics & Gynecology, University of Ioannina, Ioannina, Epirus, Greece Division of Medical Genetics and Clinical Embryology, Department of Obstetrics & Gynecology, University Hospital of Ioannina, Ioannina, Epirus, Greece ix

10 x Contributors Monika Gullerova, Ph.D. Sir William Dunn School of Pathology, University of Oxford, Oxford, UK Michalis Hadjithomas, B.Sc., Ph.D. DOE Joint Genome Institute, Walnut Creek, CA, USA Lawrence Berkeley National Laboratory, Berkeley, CA, USA Paul Kalitsis, Ph.D. Murdoch Childrens Research Institute, Royal Children s Hospital, Parkville, VIC, Australia Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia Costas Koufaris, Ph.D. Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus Penelope Kroustallaki, B.Sc., M.Sc. Department of Experimental Medicine and Translational Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece Paris Ladias, B.Sc. Division of Reproductive Genetics, Department of Obstetrics & Gynecology, University of Ioannina, Ioannina, Epirus, Greece Leandros Lazaros, Ph.D. Division of Reproductive Genetics, Department of Obstetrics & Gynecology, University of Ioannina, Ioannina, Greece Laboratory of Medical Genetics and Clinical Embryology, Department of Obstetrics & Gynecology, University Hospital of Ioannina, Ioannina, Epirus, Greece Sofi a Markoula, M.D., Ph.D. Department of Neurology, University Hospital of Ioannina, Ioannina, Epirus, Greece Francisco Martínez-Abarca, Ph.D. Grupo de Ecología Genética, Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín/Consejo Superior de Investigaciones Científicas, Granada, Spain María Dolores Molina-Sánchez, Ph.D. Grupo de Ecología Genética, Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín/ Consejo Superior de Investigaciones Científicas, Granada, Spain Rafael Nisa-Martínez, Ph.D. Grupo de Ecología Genética, Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín/Consejo Superior de Investigaciones Científicas, Granada, Spain Gregory Papagregoriou, Ph.D. Department of Biological Sciences, Molecular Medicine Research Center, University of Cyprus, Nicosia, Cyprus Carolina Sismani, Ph.D. Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus Sotirios S. Tezias, M.Sc. Laboratory of Pharmacology, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece

11 Contributors xi Nicolás Toro, Ph.D. Grupo de Ecología Genética, Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín/Consejo Superior de Investigaciones Científicas, Granada, Spain Ioannis S. Vizirianakis, Ph.D. Laboratory of Pharmacology, Department of Pharmaceutical Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece Konstantinos Voskarides, Ph.D. Department of Biological Sciences, Molecular Medicine Research Center, University of Cyprus, Nicosia, Cyprus