RNA RegulationHuy SengMay 13, 2008CS374 - Algorithms in BiologyCentral Dogma ofMolecular Biologyhttp://www.uta.edu/biology/henry/classnotes/2457/Central%20Dogma.jpgMessenger RNA (mRNA)http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/images/mrna.gif• Encodes a chemicalblueprint for protein product• Transcribed from DNAtemplate and carries codinginfo to ribosomes• Genetic info encoded in seqof 4 nucleotides arrangedinto codons of 3 bases each• Each codon encodes for aspecific amino acid, exceptstop codons• Requires tRNA and rRNATransfer RNA (tRNA)http://www.wiley.com/legacy/college/boyer/0470003790/structure/tRNA/trna_diagram.gif• Small RNA (about 74-95nucleotides)• Transfers specific AA togrowing polypeptide chainat ribosomal site ofprotein synthesis duringtranslation• 3’ terminal site for AAattachment• 3-base region calledanticodon that pairs withcodon region on mRNARibosomal RNA (rRNA)http://www.steve.gb.com/images/science/5s_rrna_predicted_secondary_structure.png• Central component ofribosome• Provides mechanismfor decoding mRNAinto AA and tointeract w/ tRNAsduring translationGenes Encode ProteinsProkaryotehttp://www.prokaryote.com/prokaryote.jpgE. Coli• >200 non-protein-coding RNA genes• Only 0.5% of totalnumber of genes• 0.2% oftranscriptionaloutputhttp://www.universityofcalifornia.edu/everyday/agriculture/images/e_coli.jpgGenes Encode ProteinsHigher Organismhttp://ai.stanford.edu/~serafim/Non-coding:Protein-coding DNA rises as aFunction of Developmental Complexity1.0Blue = prokaryotes Green = plants Red = vertebratesBlack = simple eukaryotes Purple = non-chordate invertebratesGray = Neurospora crassa Yellow = Ciona intestinalisHow does regulation scalewith complexity?Log(total # of genes)Log(genes that encode regulatory proteins)Simplified Biological Historyof the EarthIntrons• 95-97% of average protein-coding gene in humans• Protein-coding sequencesoccupy 1.5% of genome• At least 1/3 of genomemust be transcribed• Widely believed thatintronic RNA is non-functional• Possible that introns aregenetically active andintronic RNA feeds geneticinformation into cell’sregulatory networkhttp://upload.wikimedia.org/wikipedia/commons/0/07/Gene.pngSplicinghttp://upload.wikimedia.org/wikipedia/commons/1/17/Pre-mRNA_to_mRNA.png• Modification of RNA after transcription• Introns removed, exons joined• Needed for typical eukaryotic mRNA before itcan be correctly translatedAlternative Splicinghttp://upload.wikimedia.org/wikipedia/commons/9/91/AlternativeSplicing.png• Variation mechanism whereexons of primary genetranscript, pre-mRNA, areseparated and reconnected toproduce alternativeribonucleotide arrangements• Synthesize greater variety ofproteins• Leads to modification of thedef. of a “gene” DNA sequence coding forthe pre-mRNA additional DNA code orother regulating processwhich regulates thealternative splicingNon- Protein-Coding RNAs(ncRNAs)• Derived from introns of protein-coding genes and introns and exonsof non-protein-coding genes• Believed to constitute the majority ofgenomic programming in higherorganismsSmall Nucleolar RNA(snoRNA)http://upload.wikimedia.org/wikipedia/commons/a/a3/RF00071.jpgC/D box snoRNAhttp://upload.wikimedia.org/wikipedia/commons/b/b8/RF00265.jpgH/ACA box snoRNA• Guide chemical modifications of rRNAs,tRNAs, and snRNAs• Commonly referred to as guide RNAsMicroRNA (miRNA)http://upload.wikimedia.org/wikipedia/commons/a/a7/Microrna_secondary_structure.png• Single-stranded RNA moleculesof about 21-23 nucleotides inlength, which regulate geneexpression• Encoded by genes that aretranscribed from DNA but nottranslated into protein• Processed from primarytranscripts known as pri-miRNAto short stem-loop structures callpre-miRNA, and finally tofunctional miRNA• Main function is todownregulate gene expressionWhat if introns arefunctional?• Genetic OS of complex eukaryotes are moresophisticated than that of simple prokaryotes• Genes evolved to produce RNA signals as higher-order regulators• ncRNAs will be processed into numerous smallersignals to influence chromatin architecture,transcription, alternative splicing, translationalefficiency, and RNA stability• Since these RNA molecules are unlikely catalytic,they’re most likely regulatory• ncRNAs convery sequence-specific signals to theirtargetsRNA Regulation• Challenging the dogma: the hiddenlayer of non-protein-coding RNAs incomplex organismsMattick, John S. BioEssays 25:930-939, 2003.• RNA regulation: a new genetics?Mattick, John S. Nature ReviewGenetics 2004.Assertions1. Majority of genomic sequences in higherorganisms (non-protein-coding DNA) isdevoted to control of developmentalprogramming2. Majority of regulatory transactions in higherorganisms conveyed by RNAs, not proteins,but regulatory controls work in concert3. Combinatorics of protein regulatorsintersecting with environmental signalsprovides insufficient state information forprogramming of differentiation anddevelopmentHypotheses• Protein signaling provides contextual cuesto guide and tune the RNA-directedpathways by providing positionalinformation and correcting stochasticerrors.• Main output of complex organism genomesis genetically active but non-coding RNA(ncRNA)• Principal advance in complex organisms wasdevelopment of digital programming systembased on ncRNA signalingncRNAs Comprise Vast Majority ofGenomic Output in Complex Organisms• 97-98% of human genome is ncRNA• Intronic RNA makes up 95% ofprimary protein-coding transcripts(pre-mRNAs)• Most miRNAs come from intergenicregions that weren’t recognized asbeing transcribed• Transcription levels of humanchromosomes 21 and 22 is an orderof magnitude higher than can beaccounted for by known or predictedexonshttp://www.biotechnologyonline.gov.au/images/contentpages/trisomy21.jpghttp://scienceblogs.com/grrlscientist/2007/06/genetic_collaboration_in_genom.phpncRNAs in Drosophila• Intron:exon ration ~1:1• Significant proportionof ncRNAs• 3/7 major transcriptsin bithorax-abdominalAB region encodeproteins but all 7 aredevelopmentallyregulated• Deletion of DNA thatencodes other regionscauses phenotypicconsequencesKnown ncRNAs• Pgc - required for germ cell formation in Drosophila• 7H4, BC1, Bsr, Ntab - expressed in particular celltypes in rat nervous system• Adapt33 - induced by oxidants in hamster HA-1 cells• BC200 - expressed specifically in neuronal cells inprimates• Bic•
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