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Hunting RNA Motifs Hunting RNA motifs Paul Gardner July 23, 2012 Paul Gardner Hunting RNA motifs Classification problems I What is this? I The second most abundant M. tuberculosis transcript I No hits to Rfam, no homologs have been identified, no known function Mycobacteria tuberculosis genome: RNA−seq and annotations 7e+05 +ve strand R ank R eads Gene −ve strand 6e+05 1 5,741K SSU rR N A 2 689K sRNA/RUF? 5e+05 3 236K R N aseP R N A 4e+05 4 197K LSU rR N A 5 119K AT P synthase 3e+05 Read counts 6 119K HSP X 2e+05 7 115K tmR N A CDSs ncRNAs 8 103K Secreted protein 1e+05 Pfam domain terminators 0e+00 Arnvig et al. Rv3661 miscrna00343 (2011) PLoS HAD Rv3662c Pathog. 4099500 4100000 4100500 4101000 4101500 4102000 genome coordinate Paul Gardner Hunting RNA motifs Classification problems I What about this? I The seventh most abundant N. gonorrhoeae transcript I No hits to Rfam, no homologs have been identified, no known function Neisseria gonorrhoeae genome: RNA−seq and annotations R ank R eads Gene 80000 +ve strand −ve strand 1 206K R N aseP R N A 2 178K tR N A -Ser 60000 3 130K ZapA 3‘ U T R ? 4 120K P hage protein 40000 5‘ U T R ? 5 97K tmR N A Read counts 6 93K BRO protein 20000 CDSs ncRNAs 7 81K sR N A ? Pfam domain terminators 8 81K Hsp70 protein 0 9 76K tRNA-Asp NGO2161 terminator12061 terminator12063 Inositol_P terminator12062 NGO2162 terminator12064 Isabella & Clark SEC−C (2011) BMC Genomics. 2137500 2138000 2138500 2139000 genome coordinate Paul Gardner Hunting RNA motifs Classification problems I And this? I The ninth most abundant C. difficile transcript I No hits to Rfam, no homologs have been identified, no known function Clostridium difficile genome: RNA−seq and annotations R ank R eads Gene 1 12K R N aseP R N A +ve strand 4000 −ve strand 2 12K 6S R N A 3 12K SR P R N A 4 11K ldhA 3000 5 10K tmR N A 6 6K spoV G 2000 7 6K Gly reductase Read counts 8 5K slpA 1000 9 4K sRNA/RUF? CDSs ncRNAs Pfam domain terminators 10 4K hypothetical prot. 11 4K sRNA/RUF? 0 terminator0881 Deakin, Lawley toxB toxB toxB terminator1760 trpS et al. (2012) 3014000 3014500 3015000 3015500 3016000 3016500 3017000 Unpublished. genome coordinate Paul Gardner Hunting RNA motifs Classification problems I And this? I The eleventh most abundant C. difficile transcript I No hits to Rfam, no homologs have been identified, no known function Clostridium difficile genome: RNA−seq and annotations R ank R eads Gene 4000 1 12K R N aseP R N A +ve strand −ve strand 2 12K 6S R N A 3 12K SR P R N A 3000 4 11K ldhA 5 10K tmR N A 6 6K spoV G 2000 7 6K Gly reductase Read counts 8 5K slpA 1000 9 4K sRNA/RUF? CDSs ncRNAs Pfam domain terminators 10 4K hypothetical prot. 11 4K sRNA/RUF? 0 Deakin, Lawley feoA2 terminator1637terminator1105 acetyltransferase et al. (2012) 1760600 1760800 1761000 1761200 1761400 1761600 Unpublished. genome coordinate Paul Gardner Hunting RNA motifs What is our next big challenge? I Past: I How many non-coding RNA genes are there? I Future: I Can we determine the functions, if any, for large sets of given RNAs? Paul Gardner Hunting RNA motifs Will a \periodic table of RNA" be useful? I My aim is to build an analog to the Periodic Table for classifying RNA families and motifs, enabling researchers to predict function. b ase b asep air YR R R R UY A R A R Y G UC R R R G U C A A G A U R R R C G C U G U G A Y R Y G C G C G G C R Y R C G R Y R C A A G G U A G C A G C A G A A G R Y R Y G G A Y C U A Y C G A U A U R R R Y R C G R U R C G 5´ 5´ 5´ 5´ 5´ 5´ 5´ 5´ ANYA GNRA UNCG T loop U t u r n k t r n 1 k t r n 2 tw ist R Y R R C Y A Y Y G R R R R G R Y G A A R Y G G A G A A U A C G G C G R A U G A Y Y R G Y A C G A Y R A Y R Y R Y C U A G A G A G R Y G U Y R A Y R Y A A R Y C G A Y R A Y G Y G C G Y R Y G C C U A R A U R Y A R C G R Y R Y R G C C A U Y A U G U A U A U C G R Y A U A U R U Y Y G R 5´ R Y A U R U 5´ R GA R RA 5´ 5´ 5´ 5´ 5´ U Y U Y 5´ U UU Y sar r ic1 sar r ic2 UAA GAN C sr C loop d om V t er m 1 t er m 2 Y G Y C U R Y G G Y R Y Y Y U U Y Y Y Y A C R Y R Y Y A Y C C Y U G R Y R R C G Y U Y R C G C G C GU C A R A R A Y A Y R Y R A C Y A U G Y Y A Y R G R R G 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G U R Y A A U C Y R G C U G R Y A U Y R R Y Y R Y R G C A U A U R U G U G C U R Y R C G Y R U A Y G Y R Y Y Y R G C U G U A R U C G U G Y R G C G C Y A C G A U C G Y G C R C G G C Y R Y R G Y R Y 5´ G C G C U A Y A A U Y Y C G G C Y R Y R G C Y 5´ 5´ AC 5´ U 5´ UC R U 5´ Y R R Y GY UYR R Y 5´ R 5´ R YY YY RRR R 5´ 5´ GC 5´ CY G Y C G G 5´ Y YY Y R R G Y YY GGY 5´ Y AA R U GG UY 5´ 5´ U U U Y 5´ Y 5´ YY 5´ TRIT IRE SECIS m ir -T A R m ir -30 m ir -9 lin -4 m ir -5 m ir -8 m ir -1 m ir -2 m ir -6 let -7 Y RNA 6S 5S t R N A R N aseP AA U AA U A A CC C U Y Y C U U U Y Y Y G C C C Y G CG AG Y Y Y R C C G C U YY Y G A C G RR GG U C CU Y G C C R R C A G A R U G C A U G C C G C U R Y U A U C R GR C G C G U A G C G C G G C U G G U 5´ Y R U U UUUUUU U A G R GR G CA CGGG A G U A U C U G C G CA G C U G C Y G C G C CC Y G GG A C R R C C A U C G G Y Y Y C A G G CGAAU U A U R A G C A U U U GG R Y R A A C Y A A A U C Y Y R U C U U C G U A A U R Y G G C A U A G G Y G U A A A U C Y C G C C Y C C U C R Y 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