ncRNAsWhat Genomes are Telling Us

ncrna.ppt

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

The ncRNAs We Know and Love

•snRNAs

•rRNAs

•tRNAs

•Snurp RNAs

•7SL RNA

•snoRNAs

•Telomerase RNA

•Xist RNA

•Vault RNA

•miRNAs

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

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

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

LSU-SSU rRNA gene repeat:

150-200 copies on HSA 13p, 14p, 15p,

21p, 22p

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-Box snoRNAs 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

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

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

Dude!

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

RISCRNA

induced silencing complex

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

http://emboj.oupjournals.org/content/vol21/issue17/images/large/cdf476f7.jpeg

A Few Parting Words on cRNAs and their Genes