1. ncRNAs What Genomes are Telling Us ncrna.ppt

2. ncRNA genes are difficult to discover! • small • an annotational and statistical concern • no ORFs and no polyadenylation • must be identified by paralogy/orthology • novel members not readily discovered from sequence • Draft or complete; no structural information; underrepresentation • draft sequence biased against tandem ncRNA gene units • “low complexity” BACs not sequenced for draft • many pseudogenes and retropseudogenes • difficult to distinguish gene from pseudogene • except tRNA genes

3. The ncRNAs We Know and Love • snRNAs • rRNAs • tRNAs • Snurp RNAs • 7SL RNA • snoRNAs • Telomerase RNA • Xist RNA • Vault RNA • miRNAs

4. Transfer RNAs (tRNAs) • About 500 genes, about 300 pseudogenes • Included tRNASeCys-UGA • Fly < Humans < Worm • Related to developmental and tissue-specific needs, not organismal complexity • tRNAaa gene number roughly correlates with aa frequency and codon bias

6. Genomic distribution of tRNA genes in human • Nonrandom dispersal (clustering) • 25% (140) located in 4 Mb of HSA6 • 0.1% of genome has near complete set of anticodons • 18 of 30 tRNAcys genes located in 0.5MB of HSA7 • Many tRNAarg and tRNAglu are loosely clustered on HSA1 • Over 50% (280) genes located on HSA1&6 • HSA3,4,8,9,10,12,18,20,21 and X have <10 tRNA genes each • HSA22 and Y have one pseudogene each and no genes

7. Ribosomal RNAs (rRNAs) • Four RNA molecules for each of two ribosome subunits • LSU rRNA = 28S, 5.8S • SSU rRNA = 18S • 5S rRNA (also part of LSU but from separate gene) • LSU and SSU rRNA genes occur as 44kb tandem repeat unit • 150-200 copies on the short arms of acrocentric chromosomes 13, 14, 15, 21, 22 • 5S rRNA gene occurs in several 200-300-unit tandem arrays • Largest at 1q41.11-1q42.13 • 2000 copies predicted; 520 pseudogenes likely

8. LSU-SSU rRNA gene repeat: 150-200 copies on HSA 13p, 14p, 15p, 21p, 22p

9. Small nucleolar RNAs (snoRNAs) • direct postranscriptional modification and processing of rRNAs in nucleolus • Two families of snoRNA genes • C/D-Box snoRNAs direct 2’-O-ribose methylations (105-107 instances) • H/ACA-BoxsnoRNAs direct pseudouridylation (95 instances) • 97 snoRNA genes • Distributed across chromosomes as nearly all single copies • 5-10 copies of CD-Box snoRNA gene inverted repeats at 17q21 • More predicted • Sequences diverse; cannot depend on paralogy to predict

13. Spliceosomal snRNAs (snurps) • Ten known RNAs (U1-U12) responsible for hnRNA splicing • Snurp RNAs either clustered or dispersed: • 44 dispersed genes for U6 RNA • 16 dispersed genes for U1 RNA • 10-20 tandem copies U2 RNA genes (6.1 kb units) at 17q21 • 30 copy loose cluster of U1 RNA genes at 1p36 • More predicted • Tandem-arrayed clusters underrepresented in draft

14. ncRNA pseuodgenes • 100’s-1000’s of pseudogene copies of ncRNA genes • More copies from ncRNAs transcribed by RNA polymerase III • Including snurp U6, 7 SL RNA, and hY RNA • Most presumed to have arisen by reverse transcription and retroposition • Like Alu and tRNA-family repeats • Analytical comparison with Alus may help explain requirements for SINE proliferation in genomes

17. Dude!

18. Small interfering RNAs (siRNAs) • siRNA-containing transcripts exhibit extensive folding • dsRNA folds recognized by DICER enzyme • siRNA molecules excised from folds in nucleus or cytoplasm • snRNA perform multiple functions • Directed degredation of specific mRNAs • Maintenance of heterochromatin • Analogous to RNAi experiments, but siRNA is endogenous

19. RISC RNA induced silencing complex

20. microRNAs (miRNAs) • ~21 nts long • “mature” miRNA • miRNAs derive from 60-80 nt dsRNA hairpins • miRNAs excised from hairpins in cytoplasm • Excised by DICER • Hairpins derive from long primary transcripts • Hairpins excised from primaries in nucleus • Some transcripts have exon-intron structure • miRNAs can derive from instron or exon sequence • Some transcripts contain clusters of miRNAs • Conserved sequence • 50% have Fugu and Danio homologues • 25% have C. elegans homologues • Primary function believed to be translational suppression • Binds to target mRNAs at 3’ ends • Suppresses, slows, or eliminates specific protein synthesis • Some act as siRNAs

27. A Few Parting Words on cRNAs and their Genes