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ncRNAs. What 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

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Ncrnas

ncRNAs

What Genomes are Telling Us

ncrna.ppt


Ncrna genes are difficult to discover
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

    The ncRNAs We Know and Love

    • snRNAs

    • rRNAs

    • tRNAs

    • Snurp RNAs

    • 7SL RNA

    • snoRNAs

    • Telomerase RNA

    • Xist RNA

    • Vault RNA

    • miRNAs


    Transfer rnas trnas
    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
    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
    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
    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


  • Spliceosomal snrnas snurps
    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
    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



  • Small interfering rnas sirnas
    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


  • RISC

    RNA

    induced

    silencing

    complex


    Micrornas mirnas
    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



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