Computational aspects of ncrna research. Mihaela Zavolan Biozentrum, Basel Swiss Institute of Bioinformatics
|
|
- Constance Daniel
- 6 years ago
- Views:
Transcription
1 Computational aspects of ncrna research Mihaela Zavolan Biozentrum, Basel Swiss Institute of Bioinformatics
2 Computational aspects on ncrna Bacterial ncrnas research Gene discovery Target discovery Discovery of transcription regulatory elements for ncrnas
3 Computational aspects on ncrna mirnas research Gene discovery: automated annotation gene prediction Expression profiling: sample comparisons visualization Target discovery: modeling mirna-mrna target interaction Characterization of regulatory networks involving RNAs: mirna target prediction prediction of transcription regulatory elements
4 Computational aspects on ncrna sirnas: design research Optimization of silencing efficacy Minimization of off-target effects
5 ncrna gene prediction Main feature: RNA secondary structure is important. Look for evidence of selection on the secondary structure. GGACaag GUCC GUGCucauGUAC GGACag GUUC GUAUuuu GUAC Identification of pairs of sites with high mutual information Proportion of mirna sequences with a P- value less than specified threshold (Bonnet et al. (2004) Bioinformatics 20:2911) Structure stabilization Mutations that are fixed in evolution preserve RNA structure (covariance models behind trnascan-se (S. Eddy), RNAalifold (I. Hofacker))
6 ncrna gene prediction Main feature: RNA secondary structure is important. Look for evidence of selection on the secondary structure mir-100 is expected to preserve its hairpin secondary structure through the various steps of mirna biogenesis.
7 Prediction of bacterial ncrnas
8 Promoter regions recognized by!70 subunit of E.coli! factor binding site TATA box
9 RNA hairpins regulate transcription termination
10 Conserved secondary structures of Vibrio ncrnas Lenz et al. - The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118:69-82 (2004).
11 mirna gene discovery Studies driven by computation 1. genome-wide computational prediction 2. validation (Lai et al., fly; Lim et al., worm; Lim et al., vertebrates; Berezikov et al., vertebrates; Pfeffer et al., viruses). Fast, incomplete. Studies driven by experiment 1. large-scale cloning 2. functional annotation 3. mirna gene prediction 4. validation (Houbaviy et al., mouse; Dostie et al., rat; Aravin et al., fly; Suh et al., man; Pfeffer et al., man, viruses). Laborious, exhaustive.
12 Functional annotation of small RNAs Sequences with known function (mrna, rrna, trna, mirna, etc.) Small (16-30 nc) cloned RNAs ALIGNMENT Genome sequence
13 Functional annotation of small RNAs Small (16-30 nc) cloned RNAs
14 Functional annotation of small RNAs Small (16-30 nc) cloned RNAs match known sequences rrna trna mirna mrna
15 Functional annotation of small RNAs Small (16-30 nc) cloned RNAs match genome multiple copies hairpin conservation Novel mirnas rrna trna mirna mrna rrna trna mirna mrna
16 Functional annotation of small RNAs Small (16-30 nc) cloned RNAs match genome multiple copies hairpin conservation Novel mirnas multiple genome matches rasirna Novel mirnas rrna trna mirna mrna rrna trna mirna mrna rrna trna mirna mrna
17 mirna gene prediction Issues: find the locations in the genome that can give rise to mirnas predict the sequence of the mature mirna Main clue: mirna precursors form stem loop structures He & Hannon (Nat. Rev. Genet. 2004)
18 ... so do many other genomic regions Fragment of proteincoding gene let-7a mir-147
19 mirna gene prediction using SVM Build a model from positive and negative examples. Detect candidate stem loops in (large) genomic sequences. Classify candidate stem loops using the model.
20 mirna gene prediction using SVM hsa-let-7c L = 84 dg = kcal/mole Nucleotide composition: A - 20% C - 19% G - 29% U - 32% Paired nucleotides: A-U - 31% G-U - 14% G-C - 29% Proportion of nucleotides in: symmetrical loops - 17% asymmetrical loops - 4% average distance between loops longest symmetrical region longest slighly asymmetrical region negative stem longest symmetrical regions longest slightly asymmetrical region L = 68 dg = kcal/mole Pfeffer et al. 2005
21 mirna gene prediction using SVM Negatives: mrnas, rrnas, trnas, viral stem loops Positives: human genomic regions containing known mirnas Features with largest negative weights: Free energy Nr. nc. in symmetrical loops in LSAR Nr. nc. in asymmetrical loops in LSAR Avg. size of asymmetrical loops Negatives Positives Features with largest positive weights: Stem length Length longest symmetrical region Nr. A-U pairs in LSAR Nr. G-C pairs in LSAR 29% false negatives 3% false positives Used SVMlight
22 Detecting candidate stem loops Search for stems whose secondary structure remains the same irrespective of their flanking sequences. example: hsa-mir % of the known human micrornas belong to such robust stems. Density of robust stems in human genome: approximately 1 every 10 kb.
23 Classification of candidate stem loops LSR L = 78 dg = 31.6 kcal/mole LSAR mirna precursor? yes: mir-ul1 of CMV (cloning frequency: 101) SVM score: 0.8
24 Application: mirna gene prediction in viruses Identification of micrornas of the herpesvirus family. Nature Methods (2005).
25 Sensitivity-specificity plots for evaluating the performance of prediction programs Sn = TP TP + FN,Sp = TP TP + FP
26 Sensitivity-specificity plots for evaluating the performance of prediction programs Sn = TP TP + FN,Sp = TP TP + FP
27 Sensitivity-specificity plots for evaluating the performance of prediction programs Sn = TP TP + FN,Sp = TP TP + FP
28 Sensitivity-specificity plots for evaluating the performance of prediction programs Sn = TP TP + FN,Sp = TP TP + FP
29 Variations on mirna gene prediction " = # w f v f f Lim, L. P. et al. (2003) Genes & Dev. 17:991
30 Variations on mirna gene prediction Berezikov, E. et al. (2005) Cell 120:21 Proportion of mirna sequences with a P- value less than specified threshold (Bonnet et al. (2004) Bioinformatics 20:2911)
31 Variations on mirna gene prediction Xie, X. et al. (2004) Nature 434:338
32 mirna gene prediction servers
33 Prediction of ncrnas using comparative genomics RNAz ( Start with an alignment of homologous sequences Compute the following features: - mean free energy of aligned sequences - structure conservation index ( SCI = E A / E ) - mean pairwise identity - number of sequences in the alignment Use a SVM to classify candidates E A is the free energy of the alignment (takes into account mutations that preserve the structure), and E is the mean free energy of aligned sequences.
34 Modeling mirna-mrna interaction for target prediction target: C.e_hbl-1 mirna : cel-let-7 target 5' U GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU mirna 3' U AU A 5' Known mirna-mrna interactions in C.elegans target: C.e._COG-1A mirna : cel-lsy-6 target 5' C CA A 3' GU CUUAUACAAAA CG GAGUAUGUUUU mirna 3' GCUUUA CA 5' target: C.e_LIN-41A mirna : cel-let-7 target 5' U AUU U 3' UUAUACAACC CUGCCUC GAUAUGUUGG GAUGGAG mirna 3' UU AU U 5' Hybrids generated using RNAhybrid
35 Modeling mirna-mrna interaction Use evolutionary conservation to determine what defines an mirna target site. Define an interaction model (e.g. the first 8 nucleotides of the mirna have to be perfectly paired with their mrna target site).
36 Modeling mirna-mrna interaction Use evolutionary conservation to determine what defines an mirna target site. Define an interaction model (e.g. the first 8 nucleotides of the mirna have to be perfectly paired with their mrna target site). Determine the locations of all candidate sites in a reference species (e.g. human).
37 Modeling mirna-mrna interaction Use evolutionary conservation to determine what defines an mirna target site. Define an interaction model (e.g. the first 8 nucleotides of the mirna have to be perfectly paired with their mrna target site). Determine the locations of all candidate sites in a reference species (e.g. human). Determine the number of these candidate sites that are conserved in a set of species that have the mirna.
38 Modeling mirna-mrna interaction Use evolutionary conservation to determine what defines an mirna target site. Define an interaction model (e.g. the first 8 nucleotides of the mirna have to be perfectly paired with their mrna target site). Determine the locations of all candidate sites in a reference species (e.g. human). Determine the number of these candidate sites that are conserved in a set of species that have the mirna. Compare with the number of conserved candidate sites that we get for a random mirna that has approximately the same number of predicted sites in the species of reference.
39 Modeling mirna-mrna interaction Use evolutionary conservation to determine what defines an mirna target site. Define an interaction model (e.g. the first 8 nucleotides of the mirna have to be perfectly paired with their mrna target site). Determine the locations of all candidate sites in a reference species (e.g. human). Determine the number of these candidate sites that are conserved in a set of species that have the mirna. Compare with the number of conserved candidate sites that we get for a random mirna that has approximately the same number of predicted sites in the species of reference. Lewis et al. 2005
40 Modeling mirna-mrna interaction S/N ratio Interaction model Some mirnas have hundreds of targets but many do not.
41 mirna target prediction servers
42 sirna design Empirical rules for sirna design - derived from the work in the Tuschl Lab (sirna user s guide:
43 sirna design Refining the rules by analyzing large datasets of sirnas (Reynolds et al. 2004, many others): different sirnas for the same gene can have markedly different silencing efficiencies.
44 sirna design S<50% S>50% S>80% S>95% +1 +1/A
45 sirna design Accesibility of target site influences sirna efficacy: Far et al. (2003) Nucl. Acids Res. 31:4417 Target accessibility prediction server
RNA Structure and the Versatility of RNA. Mitesh Shrestha
RNA Structure and the Versatility of RNA Mitesh Shrestha Ribonucleic Acid (RNA) Nitrogenous Bases (Adenine, Uracil, Guanine, Cytosine) Ribose Sugar Ribonucleic Acid (RNA) Phosphate Group RNA world Hypothesis
More informationRNA Interference (RNAi) (see also sirna, micrna, shrna, etc.)
Biochemistry 412 RNA Interference (RNAi) (see also sirna, micrna, shrna, etc.) April 3, 2007 The Discovery of the RNA Interference (RNAi) Phenomenon 1. Gene-specific inhibition of expression by anti-sense
More informationRNA Secondary Structure Prediction Computational Genomics Seyoung Kim
RNA Secondary Structure Prediction 02-710 Computational Genomics Seyoung Kim Outline RNA folding Dynamic programming for RNA secondary structure prediction Covariance model for RNA structure prediction
More informationRNA Interference (RNAi) (see also mirna, sirna, micrna, shrna, etc.)
Biochemistry 412 RNA Interference (RNAi) (see also mirna, sirna, micrna, shrna, etc.) April 8, 2008 The Discovery of the RNA Interference (RNAi) Phenomenon 1. Gene-specific inhibition of expression by
More informationGenetic Variability of MicroRNA Genes in 15 Animal Species
51 Ivyspring International Publisher Research Paper Journal of Genomics 2015; 3: 51-56. doi: 10.7150/jgen.11246 Genetic Variability of MicroRNA Genes in 15 Animal Species Minja Zorc, Jana Obsteter, Peter
More informationThemes: RNA and RNA Processing. Messenger RNA (mrna) What is a gene? RNA is very versatile! RNA-RNA interactions are very important!
Themes: RNA is very versatile! RNA and RNA Processing Chapter 14 RNA-RNA interactions are very important! Prokaryotes and Eukaryotes have many important differences. Messenger RNA (mrna) Carries genetic
More informationRNA secondary structure prediction and analysis
RNA secondary structure prediction and analysis 1 Resources Lecture Notes from previous years: Takis Benos Covariance algorithm: Eddy and Durbin, Nucleic Acids Research, v22: 11, 2079 Useful lecture slides
More informationDNA Transcription. Dr Aliwaini
DNA Transcription 1 DNA Transcription-Introduction The synthesis of an RNA molecule from DNA is called Transcription. All eukaryotic cells have five major classes of RNA: ribosomal RNA (rrna), messenger
More informationThermo Scientific Dharmacon SMARTvector 2.0 Lentiviral shrna Particles
Thermo Scientific Dharmacon SMARTvector 2.0 Lentiviral shrna Particles Long-term gene silencing shrna-specific design algorithm High titer, purified particles Thermo Scientific Dharmacon SMARTvector shrna
More informationDNA Transcription. Visualizing Transcription. The Transcription Process
DNA Transcription By: Suzanne Clancy, Ph.D. 2008 Nature Education Citation: Clancy, S. (2008) DNA transcription. Nature Education 1(1) If DNA is a book, then how is it read? Learn more about the DNA transcription
More informationGene Expression and Heritable Phenotype. CBS520 Eric Nabity
Gene Expression and Heritable Phenotype CBS520 Eric Nabity DNA is Just the Beginning DNA was determined to be the genetic material, and the structure was identified as a (double stranded) double helix.
More informationWORKING WITH THE FIGURES. 1. In Figure 8-3, why are the arrows for genes 1 and 2 pointing in opposite directions?
8 RNA: Transcription and Processing WORKING WITH THE FIGURES 1. In Figure 8-3, why are the arrows for genes 1 and 2 pointing in opposite directions? The arrows for genes 1 and 2 indicate the direction
More informationName Class Date. Practice Test
Name Class Date 12 DNA Practice Test Multiple Choice Write the letter that best answers the question or completes the statement on the line provided. 1. What do bacteriophages infect? a. mice. c. viruses.
More informationChapter 8 Lecture Outline. Transcription, Translation, and Bioinformatics
Chapter 8 Lecture Outline Transcription, Translation, and Bioinformatics Replication, Transcription, Translation n Repetitive processes Build polymers of nucleotides or amino acids n All have 3 major steps
More informationRNA does not adopt the classic B-DNA helix conformation when it forms a self-complementary double helix
Reason: RNA has ribose sugar ring, with a hydroxyl group (OH) If RNA in B-from conformation there would be unfavorable steric contact between the hydroxyl group, base, and phosphate backbone. RNA structure
More informationOptimization of RNAi Targets on the Human Transcriptome Ahmet Arslan Kurdoglu Computational Biosciences Program Arizona State University
Optimization of RNAi Targets on the Human Transcriptome Ahmet Arslan Kurdoglu Computational Biosciences Program Arizona State University my background Undergraduate Degree computer systems engineer (ASU
More informationBIOINFORMATICS ORIGINAL PAPER
BIOINFORMATICS ORIGINAL PAPER Vol. 28 no. 4 2012, pages 457 463 doi:10.1093/bioinformatics/btr687 Genome analysis Advance Access publication December 9, 2011 Identifying small interfering RNA loci from
More informationTaqMan Advanced mirna Assays
PRODUCT BULLETIN TaqMan Advanced mirna Assays TaqMan Advanced mirna Assays Key features Universal reverse transcription (RT) one RT step for all Applied Biosystems TaqMan Advanced mirna Assays Sensitive
More information90 Algorithms in Bioinformatics I, WS 06, ZBIT, D. Huson, December 4, 2006
90 Algorithms in Bioinformatics I, WS 06, ZBIT, D. Huson, December 4, 2006 8 RNA Secondary Structure Sources for this lecture: R. Durbin, S. Eddy, A. Krogh und G. Mitchison. Biological sequence analysis,
More informationThe Genetic Code and Transcription. Chapter 12 Honors Genetics Ms. Susan Chabot
The Genetic Code and Transcription Chapter 12 Honors Genetics Ms. Susan Chabot TRANSCRIPTION Copy SAME language DNA to RNA Nucleic Acid to Nucleic Acid TRANSLATION Copy DIFFERENT language RNA to Amino
More informationTERTIARY MOTIF INTERACTIONS ON RNA STRUCTURE
1 TERTIARY MOTIF INTERACTIONS ON RNA STRUCTURE Bioinformatics Senior Project Wasay Hussain Spring 2009 Overview of RNA 2 The central Dogma of Molecular biology is DNA RNA Proteins The RNA (Ribonucleic
More informationRNA-Sequencing analysis
RNA-Sequencing analysis Markus Kreuz 25. 04. 2012 Institut für Medizinische Informatik, Statistik und Epidemiologie Content: Biological background Overview transcriptomics RNA-Seq RNA-Seq technology Challenges
More informationProduct Applications for the Sequence Analysis Collection
Product Applications for the Sequence Analysis Collection Pipeline Pilot Contents Introduction... 1 Pipeline Pilot and Bioinformatics... 2 Sequence Searching with Profile HMM...2 Integrating Data in a
More informationCHAPTER 21 LECTURE SLIDES
CHAPTER 21 LECTURE SLIDES Prepared by Brenda Leady University of Toledo To run the animations you must be in Slideshow View. Use the buttons on the animation to play, pause, and turn audio/text on or off.
More informationRNA metabolism. DNA dependent synthesis of RNA RNA processing RNA dependent synthesis of RNA and DNA.
RNA metabolism DNA dependent synthesis of RNA RNA processing RNA dependent synthesis of RNA and DNA http://www.youtube.com/watch?v=ovc8nxobxmq DNA dependent synthesis of RNA : production of an RNA molecule
More informationGalina Gabriely, Ph.D. BWH/HMS
Galina Gabriely, Ph.D. BWH/HMS Email: ggabriely@rics.bwh.harvard.edu Outline: microrna overview microrna expression analysis microrna functional analysis microrna (mirna) Characteristics mirnas discovered
More informationWhole Transcriptome Analysis of Illumina RNA- Seq Data. Ryan Peters Field Application Specialist
Whole Transcriptome Analysis of Illumina RNA- Seq Data Ryan Peters Field Application Specialist Partek GS in your NGS Pipeline Your Start-to-Finish Solution for Analysis of Next Generation Sequencing Data
More informationYear III Pharm.D Dr. V. Chitra
Year III Pharm.D Dr. V. Chitra 1 Genome entire genetic material of an individual Transcriptome set of transcribed sequences Proteome set of proteins encoded by the genome 2 Only one strand of DNA serves
More informationIDENTIFICATION AND CLASSIFICATION OF SMALL RNAS IN TRANSCRIPTOME SEQUENCE DATA
September 23, 2009 :23 WSPC - Proceedings Trim Size: in x 8.5in Langenberger Pacific Symposium on Biocomputing 5:80-87(200) IDENTIFICATION AND CLASSIFICATION OF SMALL RNAS IN TRANSCRIPTOME SEQUENCE DATA
More informationTranscription in Eukaryotes
Transcription in Eukaryotes Biology I Hayder A Giha Transcription Transcription is a DNA-directed synthesis of RNA, which is the first step in gene expression. Gene expression, is transformation of the
More informationEukaryotic Gene Structure
Eukaryotic Gene Structure Terminology Genome entire genetic material of an individual Transcriptome set of transcribed sequences Proteome set of proteins encoded by the genome 2 Gene Basic physical and
More informationLaboratoire IBISC. Biologie Intégrative et Systèmes Complexes
Laboratoire IBISC Biologie Intégrative et Systèmes Complexes A fast ab initio method for predicting mirna precursors in genomes Sébastien Tempel, Fariza Tahi IBISC University of Evry-Val d Essonne, Genopole,
More informationRNA is a single strand molecule composed of subunits called nucleotides joined by phosphodiester bonds.
The Versatility of RNA Primary structure of RNA RNA is a single strand molecule composed of subunits called nucleotides joined by phosphodiester bonds. Each nucleotide subunit is composed of a ribose sugar,
More informationPlants Fight it out Intrinsic defence mechanism The magic world of Gene silencing
I LOVE YOU Plants Fight it out Intrinsic defence mechanism The magic world of Gene silencing Over expression of Chalcone synthase gene to get Purple Petunias Napoli, Lemieux & Jorgensen,1990 Desired Effect
More informationGenome Sequence Assembly
Genome Sequence Assembly Learning Goals: Introduce the field of bioinformatics Familiarize the student with performing sequence alignments Understand the assembly process in genome sequencing Introduction:
More informationGene Expression: Transcription
Gene Expression: Transcription The majority of genes are expressed as the proteins they encode. The process occurs in two steps: Transcription = DNA RNA Translation = RNA protein Taken together, they make
More informationSelf-test Quiz for Chapter 12 (From DNA to Protein: Genotype to Phenotype)
Self-test Quiz for Chapter 12 (From DNA to Protein: Genotype to Phenotype) Question#1: One-Gene, One-Polypeptide The figure below shows the results of feeding trials with one auxotroph strain of Neurospora
More informationConcepts and Methods in Developmental Biology
Biology 4361 Developmental Biology Concepts and Methods in Developmental Biology June 16, 2009 Conceptual and Methodological Tools Concepts Genomic equivalence Differential gene expression Differentiation/de-differentiation
More informationGenetics - Problem Drill 19: Dissection of Gene Function: Mutational Analysis of Model Organisms
Genetics - Problem Drill 19: Dissection of Gene Function: Mutational Analysis of Model Organisms No. 1 of 10 1. The mouse gene knockout is based on. (A) Homologous recombination (B) Site-specific recombination
More informationsirna Overview and Technical Tips
1 sirna Overview and Technical Tips 2 CONTENTS 3 4 5 7 8 10 11 13 14 18 19 20 21 Introduction Applications How Does It Work? Handy Tips Troubleshooting Conclusions Further References Contact Us 3 INTRODUCTION
More informationCOMPUTATIONAL DISCOVERY OF ANIMAL SMALL RNA GENES AND TARGETS. Inauguraldissertation. zur. Erlangung der Würde eines Doktors der Philosophie
COMPUTATIONAL DISCOVERY OF ANIMAL SMALL RNA GENES AND TARGETS Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der
More informationUCSC Genome Browser. Introduction to ab initio and evidence-based gene finding
UCSC Genome Browser Introduction to ab initio and evidence-based gene finding Wilson Leung 06/2006 Outline Introduction to annotation ab initio gene finding Basics of the UCSC Browser Evidence-based gene
More informationNon-Organic-Based Isolation of Mammalian microrna using Norgen s microrna Purification Kit
Application Note 13 RNA Sample Preparation Non-Organic-Based Isolation of Mammalian microrna using Norgen s microrna Purification Kit B. Lam, PhD 1, P. Roberts, MSc 1 Y. Haj-Ahmad, M.Sc., Ph.D 1,2 1 Norgen
More informationBio11 Announcements. Ch 21: DNA Biology and Technology. DNA Functions. DNA and RNA Structure. How do DNA and RNA differ? What are genes?
Bio11 Announcements TODAY Genetics (review) and quiz (CP #4) Structure and function of DNA Extra credit due today Next week in lab: Case study presentations Following week: Lab Quiz 2 Ch 21: DNA Biology
More informationMATH 5610, Computational Biology
MATH 5610, Computational Biology Lecture 2 Intro to Molecular Biology (cont) Stephen Billups University of Colorado at Denver MATH 5610, Computational Biology p.1/24 Announcements Error on syllabus Class
More informationComparison of Commercial Transfection Reagents: Cell line optimized transfection kits for in vitro cancer research.
Comparison of Commercial Transfection Reagents: Cell line optimized transfection kits for in vitro cancer research. by Altogen Labs, 11200 Manchaca Road, Suite 203 Austin TX 78748 USA Tel. (512) 433-6177
More informationBIOLOGY LTF DIAGNOSTIC TEST DNA to PROTEIN & BIOTECHNOLOGY
Biology Multiple Choice 016074 BIOLOGY LTF DIAGNOSTIC TEST DNA to PROTEIN & BIOTECHNOLOGY Test Code: 016074 Directions: Each of the questions or incomplete statements below is followed by five suggested
More informationM I C R O B I O L O G Y WITH DISEASES BY TAXONOMY, THIRD EDITION
M I C R O B I O L O G Y WITH DISEASES BY TAXONOMY, THIRD EDITION Chapter 7 Microbial Genetics Lecture prepared by Mindy Miller-Kittrell, University of Tennessee, Knoxville The Structure and Replication
More informationTRANSCRIPTION AND PROCESSING OF RNA
TRANSCRIPTION AND PROCESSING OF RNA 1. The steps of gene expression. 2. General characterization of transcription: steps, components of transcription apparatus. 3. Transcription of eukaryotic structural
More informationGenome Annotation Genome annotation What is the function of each part of the genome? Where are the genes? What is the mrna sequence (transcription, splicing) What is the protein sequence? What does
More informationChapter 8: DNA and RNA
Chapter 8: DNA and RNA Lecture Outline Enger, E. D., Ross, F. C., & Bailey, D. B. (2012). Concepts in biology (14th ed.). New York: McGraw- Hill. 1 8-1 DNA and the Importance of Proteins Proteins play
More informationDNA Structure and Replication, and Virus Structure and Replication Test Review
DNA Structure and Replication, and Virus Structure and Replication Test Review What does DNA stand for? Deoxyribonucleic Acid DNA is what type of macromolecule? DNA is a nucleic acid The building blocks
More informationRFMirTarget: A Random Forest Classifier for Human mirna Target Gene Prediction
RFMirTarget: A Random Forest Classifier for Human mirna Target Gene Prediction Mariana R. Mendoza 1, Guilherme C. da Fonseca 2, Guilherme L. de Morais 2, Ronnie Alves 3, Ana L.C. Bazzan 1, and Rogerio
More informationOptimizing Synthetic DNA for Metabolic Engineering Applications. Howard Salis Penn State University
Optimizing Synthetic DNA for Metabolic Engineering Applications Howard Salis Penn State University Synthetic Biology Specify a function Build a genetic system (a DNA molecule) Genetic Pseudocode call producequorumsignal(luxi
More informationSolutions to Quiz II
MIT Department of Biology 7.014 Introductory Biology, Spring 2005 Solutions to 7.014 Quiz II Class Average = 79 Median = 82 Grade Range % A 90-100 27 B 75-89 37 C 59 74 25 D 41 58 7 F 0 40 2 Question 1
More informationTOOLS sirna and mirna. User guide
TOOLS sirna and mirna User guide Introduction RNA interference (RNAi) is a powerful tool for suppression gene expression by causing the destruction of specific mrna molecules. Small Interfering RNAs (sirnas)
More informationReview of Protein (one or more polypeptide) A polypeptide is a long chain of..
Gene expression Review of Protein (one or more polypeptide) A polypeptide is a long chain of.. In a protein, the sequence of amino acid determines its which determines the protein s A protein with an enzymatic
More informationLearning Objectives. Define RNA interference. Define basic terminology. Describe molecular mechanism. Define VSP and relevance
Learning Objectives Define RNA interference Define basic terminology Describe molecular mechanism Define VSP and relevance Describe role of RNAi in antigenic variation A Nobel Way to Regulate Gene Expression
More informationGENETIC VARIABILITY OF microrna GENES IN FARM ANIMALS
20 th Int. Symp. Animal Science Days, Kranjska gora, Slovenia, Sept. 19 th 21 st, 2012. COBISS: 1.08 Agris category code: L10 GENETIC VARIABILITY OF microrna GENES IN FARM ANIMALS Daša JEVŠINEK SKOK 1,
More informationHost : Dr. Nobuyuki Nukina Tutor : Dr. Fumitaka Oyama
Method to assign the coding regions of ESTs Céline Becquet Summer Program 2002 Structural Neuropathology Lab Molecular Neuropathology Group RIKEN Brain Science Institute Host : Dr. Nobuyuki Nukina Tutor
More informationMapping strategies for sequence reads
Mapping strategies for sequence reads Ernest Turro University of Cambridge 21 Oct 2013 Quantification A basic aim in genomics is working out the contents of a biological sample. 1. What distinct elements
More information2. From the first paragraph in this section, find three ways in which RNA differs from DNA.
Name Chapter 17: From Gene to Protein Begin reading at page 328 Basic Principles of Transcription and Translation. Work on this chapter a single concept at a time, and expect to spend at least 6 hours
More informationMISSION shrna Library: Next Generation RNA Interference
Page 1 of 6 Page 1 of 6 Return to Web Version MISSION shrna Library: Next Generation RNA Interference By: Stephanie Uder, Henry George, Betsy Boedeker, LSI Volume 6 Article 2 Introduction The technology
More informationProtein Synthesis: Transcription and Translation
Protein Synthesis: Transcription and Translation Proteins In living things, proteins are in charge of the expression of our traits (hair/eye color, ability to make insulin, predisposition for cancer, etc.)
More information13.1 RNA. Lesson Objectives. Lesson Summary
13.1 RNA Lesson Objectives Contrast RNA and DNA. Explain the process of transcription. Lesson Summary The Role of RNA RNA (ribonucleic acid) is a nucleic acid like DNA. It consists of a long chain of nucleotides.
More informationSingle Cell Genomics
Single Cell Genomics Application Cost Platform/Protoc ol Note Single cell 3 mrna-seq cell lysis/rt/library prep $2460/Sample 10X Genomics Chromium 500-10,000 cells/sample Single cell 5 V(D)J mrna-seq cell
More informationTranscription & post transcriptional modification
Transcription & post transcriptional modification Transcription The synthesis of RNA molecules using DNA strands as the templates so that the genetic information can be transferred from DNA to RNA Similarity
More informationDNA RNA PROTEIN. Professor Andrea Garrison Biology 11 Illustrations 2010 Pearson Education, Inc. unless otherwise noted
DNA RNA PROTEIN Professor Andrea Garrison Biology 11 Illustrations 2010 Pearson Education, Inc. unless otherwise noted DNA Molecule of heredity Contains all the genetic info our cells inherit Determines
More informationTranscription in Prokaryotes. Jörg Bungert, PhD Phone:
Transcription in Prokaryotes Jörg Bungert, PhD Phone: 352-273-8098 Email: jbungert@ufl.edu Objectives Understand the basic mechanism of transcription. Know the function of promoter elements and associating
More information2012 GENERAL [5 points]
GENERAL [5 points] 2012 Mark all processes that are part of the 'standard dogma of molecular' [ ] DNA replication [ ] transcription [ ] translation [ ] reverse transposition [ ] DNA restriction [ ] DNA
More informationWhat happens after DNA Replication??? Transcription, translation, gene expression/protein synthesis!!!!
What happens after DNA Replication??? Transcription, translation, gene expression/protein synthesis!!!! Protein Synthesis/Gene Expression Why do we need to make proteins? To build parts for our body as
More information7.014 Quiz II 3/18/05. Write your name on this page and your initials on all the other pages in the space provided.
7.014 Quiz II 3/18/05 Your Name: TA's Name: Write your name on this page and your initials on all the other pages in the space provided. This exam has 10 pages including this coversheet. heck that you
More informationGene-centered resources at NCBI
COURSE OF BIOINFORMATICS a.a. 2014-2015 Gene-centered resources at NCBI We searched Accession Number: M60495 AT NCBI Nucleotide Gene has been implemented at NCBI to organize information about genes, serving
More informationFirePlex mirna Assay. Multiplex microrna profiling from low sample inputs
FirePlex mirna Assay Multiplex microrna profiling from low sample inputs Abstract We introduce a new assay for multiplex microrna (mirna) discovery and verification that enables simultaneous profiling
More informationMolecular Biology Primer. CptS 580, Computational Genomics, Spring 09
Molecular Biology Primer pts 580, omputational enomics, Spring 09 Starting 19 th century What do we know of cellular biology? ell as a fundamental building block 1850s+: ``DNA was discovered by Friedrich
More informationComparative Bioinformatics. BSCI348S Fall 2003 Midterm 1
BSCI348S Fall 2003 Midterm 1 Multiple Choice: select the single best answer to the question or completion of the phrase. (5 points each) 1. The field of bioinformatics a. uses biomimetic algorithms to
More informationLong and short/small RNA-seq data analysis
Long and short/small RNA-seq data analysis GEF5, 4.9.2015 Sami Heikkinen, PhD, Dos. Topics 1. RNA-seq in a nutshell 2. Long vs short/small RNA-seq 3. Bioinformatic analysis work flows GEF5 / Heikkinen
More informationMicroarray Gene Expression Analysis at CNIO
Microarray Gene Expression Analysis at CNIO Orlando Domínguez Genomics Unit Biotechnology Program, CNIO 8 May 2013 Workflow, from samples to Gene Expression data Experimental design user/gu/ubio Samples
More informationChapter 13. From DNA to Protein
Chapter 13 From DNA to Protein Proteins All proteins consist of polypeptide chains A linear sequence of amino acids Each chain corresponds to the nucleotide base sequenceof a gene The Path From Genes to
More informationmeasuring gene expression December 5, 2017
measuring gene expression December 5, 2017 transcription a usually short-lived RNA copy of the DNA is created through transcription RNA is exported to the cytoplasm to encode proteins some types of RNA
More informationComputational and Experimental Identification of C. elegans micrornas
Computational and Experimental Identification of C. elegans micrornas Yonatan Grad, 1,3 John Aach, 1,3 Gabriel D. Hayes, 2,3 Brenda J. Reinhart, 2,4 George M. Church, 1 Gary Ruvkun, 1, * and John Kim 2,3
More informationFigure S1: NUN preparation yields nascent, unadenylated RNA with a different profile from Total RNA.
Summary of Supplemental Information Figure S1: NUN preparation yields nascent, unadenylated RNA with a different profile from Total RNA. Figure S2: rrna removal procedure is effective for clearing out
More informationChapter 14 Active Reading Guide From Gene to Protein
Name: AP Biology Mr. Croft Chapter 14 Active Reading Guide From Gene to Protein This is going to be a very long journey, but it is crucial to your understanding of biology. Work on this chapter a single
More informationDo you remember. What is a gene? What is RNA? How does it differ from DNA? What is protein?
Lesson 1 - RNA Do you remember What is a gene? What is RNA? How does it differ from DNA? What is protein? Gene Segment of DNA that codes for building a protein DNA code is copied into RNA form, and RNA
More informationChapter 11: Regulation of Gene Expression
Chapter Review 1. It has long been known that there is probably a genetic link for alcoholism. Researchers studying rats have begun to elucidate this link. Briefly describe the genetic mechanism found
More informationClick here to read the case study about protein synthesis.
Click here to read the case study about protein synthesis. Big Question: How do cells use the genetic information stored in DNA to make millions of different proteins the body needs? Key Concept: Genetics
More informationDNA Topoisomerases relieve the supercoiling stress ahead of the fork
DNA Topoisomerases relieve the supercoiling stress ahead of the fork Tw 1) T w : # of turns around the central axis 2) W r : # of times the double helix crosses itself 3) Linking Number: L k = T w + W
More informationFig Ch 17: From Gene to Protein
Fig. 17-1 Ch 17: From Gene to Protein Basic Principles of Transcription and Translation RNA is the intermediate between genes and the proteins for which they code Transcription is the synthesis of RNA
More informationFundamentals of Bioinformatics: computation, biology, computational biology
Fundamentals of Bioinformatics: computation, biology, computational biology Vasilis J. Promponas Bioinformatics Research Laboratory Department of Biological Sciences University of Cyprus A short self-introduction
More informationDNA makes RNA makes Proteins. The Central Dogma
DNA makes RNA makes Proteins The Central Dogma TRANSCRIPTION DNA RNA transcript RNA polymerase RNA PROCESSING Exon RNA transcript (pre-mrna) Intron Aminoacyl-tRNA synthetase NUCLEUS CYTOPLASM FORMATION
More informationRNA Interference and the World of Small RNAs
RNA Interference and the World of Small RNAs O, I die, Horatio; The potent poison quite o'er-crows my spirit: I cannot live to hear the news from England; But I do prophesy the election lights On Fortinbras:
More informationGene Expression Transcription/Translation Protein Synthesis
Gene Expression Transcription/Translation Protein Synthesis 1. Describe how genetic information is transcribed into sequences of bases in RNA molecules and is finally translated into sequences of amino
More informationRNA : functional role
RNA : functional role Hamad Yaseen, PhD MLS Department, FAHS Hamad.ali@hsc.edu.kw RNA mrna rrna trna 1 From DNA to Protein -Outline- From DNA to RNA From RNA to Protein From DNA to RNA Transcription: Copying
More informationWhy learn sequence database searching? Searching Molecular Databases with BLAST
Why learn sequence database searching? Searching Molecular Databases with BLAST What have I cloned? Is this really!my gene"? Basic Local Alignment Search Tool How BLAST works Interpreting search results
More informationRNA and Protein Synthesis
RNA and Protein Synthesis CTE: Agriculture and Natural Resources: C5.3 Understand various cell actions, such as osmosis and cell division. C5.4 Compare and contrast plant and animal cells, bacteria, and
More informationSTUDY GUIDE SECTION 10-1 Discovery of DNA
STUDY GUIDE SECTION 10-1 Discovery of DNA Name Period Date Multiple Choice-Write the correct letter in the blank. 1. The virulent strain of the bacterium S. pneumoniae causes disease because it a. has
More informationCardioviral RNA structure logo analysis: entropy, correlations, and prediction
J Biol Phys (2010) 36:145 159 DOI 10.1007/s10867-009-9154-z ORIGINAL PAPER Cardioviral RNA structure logo analysis: entropy, correlations, and prediction Xiao-Zhou Chen Huai Cao Wen Zhang Ci-Quan Liu Received:
More informationNon-coding RNA detection and bioinformatics-based analysis. Jonathan E. Cohen, Ph.D. FAES BIOL254 February 22, 2016
Non-coding RNA detection and bioinformatics-based analysis Jonathan E. Cohen, Ph.D. FAES BIOL254 February 22, 2016 How to identify and study non-coding RNAs, e.g. mirnas? The 3 P s Your favorite experimental
More informationGENE EXPRESSION AT THE MOLECULAR LEVEL. Copyright (c) The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
GENE EXPRESSION AT THE MOLECULAR LEVEL Copyright (c) The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1 Gene expression Gene function at the level of traits Gene function
More informationWatson BM Gene Capitolo 11 Watson et al., BIOLOGIA MOLECOLARE DEL GENE, Zanichelli editore S.p.A. ? Le proteine della trasposizione Watson et al., BIOLOGIA MOLECOLARE DEL GENE, Zanichelli editore S.p.A.
More information