RNA Structure & Function: Promoter Prediction and MicroRNA Biogenesis - Prof. Drena Leigh , Exams of Bioinformatics

Download RNA Structure & Function: Promoter Prediction and MicroRNA Biogenesis - Prof. Drena Leigh and more Exams Bioinformatics in PDF only on Docsity! RNA Structure & Function 10/31/05 D Dobbs ISU - BCB 444/544X 1 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 1 10/31/05 RNA Structure & Function 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 2 Announcements Seminar (Mon Oct 31) 12:10 PM IG Faculty Seminar in 101 Ind Ed II Plant Steroid Hormone Signal Transduction Yanhai Yin, GDCB • BCB Link for Seminar Schedules (updated) http://www.bcb.iastate.edu/seminars/index.html 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 3 Announcements BCB 544 Projects - Important Dates: Nov 2 Wed noon - Project proposals due to David/Drena Nov 4 Fri 10A - Approvals/responses to students Dec 2 Fri noon - Written project reports due Dec 5,7,8,9 class/lab - Oral Presentations (20') (Dec 15 Thurs = Final Exam) 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 4 RNA Structure & Function Prediction Mon Review - promoter prediction RNA structure & function Wed RNA structure prediction 2' & 3' structure prediction miRNA & target prediction RNA function prediction? 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 5 Reading Assignment (for Mon/Wed) Mount Bioinformatics • Chp 8 Prediction of RNA Secondary Structure • pp. 327-355 • Ck Errata: http://www.bioinformaticsonline.org/help/errata2.html Cates (Online) RNA Secondary Structure Prediction Module • http://cnx.rice.edu/content/m11065/latest/ 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 6 Review last lecture: Promoter Prediction RNA Structure & Function 10/31/05 D Dobbs ISU - BCB 444/544X 2 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 7 Promoter Prediction • Overview of strategies  What sequence signals can be used?  What other types of information can be used? • Algorithms  a bit more about these in later lectures • Promoter prediction software • 3 major types • many, many programs! 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 8 Promoter prediction: Eukaryotes vs prokaryotes Promoter prediction is easier in microbial genomes Why? Highly conserved Simpler gene structures More sequenced genomes! (for comparative approaches) Methods? Previously, again mostly HMM-based Now: similarity-based. comparative methods because so many genomes available 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 9 Promoter Prediction: Steps & Strategies  Closely related to gene prediction! • Obtain genomic sequence • Use sequence-similarity based comparison (BLAST, MSA) to find related genes But: "regulatory" regions are much less well- conserved than coding regions • Locate ORFs • Identify TSS (Transcription Start Site) • Use promoter prediction programs • Analyze motifs, etc. in sequence (TRANSFAC) 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 10 Promoter Prediction: Steps & Strategies Identify TSS --if possible? • One of biggest problems is determining exact TSS! Not very many full-length cDNAs! • Good starting point? (human & vertebrate genes) Use FirstEF found within UCSC Genome Browser or submit to FirstEF web server Fig 5.10 Baxevanis & Ouellette 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 11 Promoter prediction strategies 1) Pattern-driven algorithms 2) Sequence-driven algorithms 3) Combined "evidence-based" BEST RESULTS? Combined, sequential 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 12 Promoter Prediction: Pattern-driven algorithms • Success depends on availability of collections of annotated binding sites (TRANSFAC & PROMO) • Tend to produce huge numbers of FPs • Why? • Binding sites (BS) for specific TFs often variable • Binding sites are short (typically 5-15 bp) • Interactions between TFs (& other proteins) influence affinity & specificity of TF binding • One binding site often recognized by multiple BFs • Biology is complex: promoters often specific to organism/cell/stage/environmental condition RNA Structure & Function 10/31/05 D Dobbs ISU - BCB 444/544X 5 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 25 Fig 6.2 Baxevanis & Ouellette 2005 Common structural motifs in RNA Helices Loops • Hairpin • Interior • Bulge • Multibranch Pseudoknots 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 26 RNA functions • Storage/transfer of genetic information • Structural • Catalytic • Regulatory 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 27 RNA functions Storage/transfer of genetic information • Genomes • many viruses have RNA genomes single-stranded (ssRNA) e.g., retroviruses (HIV) double-stranded (dsRNA) • Transfer of genetic information • mRNA = "coding RNA" - encodes proteins 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 28 RNA functions Structural • e.g., rRNA, which is major structural component of ribosomes (Gloria Culver, ISU) BUT - its role is not just structural, also: Catalytic RNA in ribosome has peptidyltransferase activity • Enzymatic activity responsible for peptide bond formation between amino acids in growing peptide chain • Also, many small RNAs are enzymes "ribozymes" (W Allen Miller, ISU) 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 29 RNA functions Regulatory Recently discovered important new roles for RNAs In normal cells: • in "defense" - esp. in plants • in normal development e.g., siRNAs, miRNA As tools: • for gene therapy or to modify gene expression • RNAi (used by many at ISU: Diane Bassham,Thomas Baum, Jeff Essner, Kristen Johansen, Jo Anne Powell-Coffman, Roger Wise, etc.) • RNA aptamers (Marit Nilsen-Hamilton, ISU) 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 30 RNA types & functions regulation of transcription and translation, other?? regulatory RNAs (siRNA, miRNA, etc.) mRNA processing, poly A addition <catalytic> rRNA processing/maturation/methylation snRNA - small nuclear snoRNA - small nucleolar signal recognition particle (SRP) tRNA processing <catalytic> scRNA - small cytoplasmic precursors & intermediates of mature mRNAs & other RNAs hnRNA - heterogeneous nuclear translation (protein synthesis)t-RNA - transfer translation (protein synthesis) <catalytic>rRNA - ribosomal translation (protein synthesis) regulatory mRNA - messenger Primary Function(s)Types of RNAs RNA Structure & Function 10/31/05 D Dobbs ISU - BCB 444/544X 6 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 31 Thanks to Chris Burge, MIT for following slides Slightly modified from: Gene Regulation and MicroRNAs Session introduction presented at ISMB 2005, Detroit, MI Chris Burge cburge@MIT.EDU C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 32 Expression of a Typical Eukaryotic Gene DNA … Transcription Protein Translation mRNA Splicing exon intron AAAAAAAAA Polyadenylation Protein Coding Gene Folding, Modification, Transport, Complex Assembly Protein Complex Degradation Degradation primary transcript / pre-mRNA Export For each of these processes, there is a ‘code’ (set of default recognition rules) C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 33 Gene Expression Challenges for Computational Biology • Understand the ‘code’ for each step in gene expression (set of default recognition rules), e.g., the ‘splicing code’ • Understand the rules for sequence-specific recognition of nucleic acids by protein and ribonucleoprotein (RNP) factors • Understand the regulatory events that occur at each step and the biological consequences of regulation Lots of data Genomes, structures, transcripts, microarrays, ChIP-Chip, etc. C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 34 Steps in Transcription Emerson Cell 2002 C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 35 Sequence-specific Transcription Factors • typically bind in clusters » Regulatory modules Kadonaga Cell 2004 C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 36 Sequence-specific Transcription Factors • have modular organization » Understand DNA-binding specificity Yan (ISU) A computational method to identify amino acid residues involved in protein-DNA interactions ATF-2/c-Jun/IRF-3 DNA complex Panne et al. EMBO J. 2004 C Burge 2005 RNA Structure & Function 10/31/05 D Dobbs ISU - BCB 444/544X 7 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 37 Maniatis & Reed Nature 2002 Integration of transcription & RNA processing C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 38 Early Steps in Pre-mRNA Splicing Matlin, Clark & Smith Nature Mol Cell Biol 2005 • Formation of exon-spanning complex • Subsequent rearrangement to form intron-spanning spliceosomes which catalyze intron excision and exon ligation hnRNP proteins C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 39 Alternative Splicing Matlin, Clark & Smith Nature Mol Cell Biol 2005 Wang (ISU) Genome-wide Comparative Analysis of Alternative Splicing in Plants > 50% of human genes undergo alternative splicing C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 40 Splicing Regulation Matlin, Clark & Smith Nature Mol Cell Biol 2005 ESE/ESS = Exonic Splicing Enhancers/Silencers ISE/ISS = Intronic Splicing Enhancers/Silencers C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 41 Coupling of Splicing & Nonsense-mediated mRNA Decay (NMD) Maniatis & Reed Nature 2002 C Burge 2005 10/31/05 D Dobbs ISU - BCB 444/544X: RNA Structure & Function 42 C. elegans lin-4 Small Regulatory RNA We now know that there are hundreds of microRNA genes (Ambros, Bartel, Carrington, Ruvkun, Tuschl, others) lin-4 precursor lin-4 RNA “Translational repression” V. Ambros lab lin-4 RNA target mRNA C Burge 2005