Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Export

@article{Washietl2005, abstract = {In contrast to the fairly reliable and complete annotation of the protein coding genes in the human genome, comparable information is lacking for noncoding RNAs (ncRNAs). We present a comparative screen of vertebrate genomes for structural noncoding RNAs, which evaluates conserved genomic DNA sequences for signatures of structural conservation of base-pairing patterns and exceptional thermodynamic stability. We predict more than 30,000 structured RNA elements in the human genome, almost 1,000 of which are conserved across all vertebrates. Roughly a third are found in introns of known genes, a sixth are potential regulatory elements in untranslated regions of protein-coding mRNAs and about half are located far away from any known gene. Only a small fraction of these sequences has been described previously. A comparison with recent tiling array data shows that more than 40\\% of the predicted structured RNAs overlap with experimentally detected sites of transcription. The widespread conservation of secondary structure points to a large number of functional ncRNAs and cis-acting mRNA structures in the human genome.}, author = {Washietl, Stefan and Hofacker, Ivo L. and Lukasser, Melanie and H\"{u}ttenhofer, Alexander and Stadler, Peter F.}, citeulike-article-id = {2318716}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt1144}, doi = {10.1038/nbt1144}, journal = {Nat Biotechnol}, keywords = {acid, analysis, and, animals, base, biology, chromosome, computational, conformation, conserved, dna, elements, from\_jabref, genetic, genome, govt, human, humans, introns, mapping, messenger, models, non-us, nucleic, pairing, phylogeny, regulatory, research, rna, sensitivity, sequence, specificity, statistical, support, thermodynamics, transcription, transcriptional, untranslated}, month = {Nov}, number = {11}, pages = {1383--1390}, posted-at = {2008-02-01 09:55:15}, priority = {2}, title = {Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.}, url = {10.1038/nbt1144}, volume = {23}, year = {2005} }

TY - JOUR ID - Washietl2005 L3 - citeulike-article-id:2318716 N2 - In contrast to the fairly reliable and complete annotation of the protein coding genes in the human genome, comparable information is lacking for noncoding RNAs (ncRNAs). We present a comparative screen of vertebrate genomes for structural noncoding RNAs, which evaluates conserved genomic DNA sequences for signatures of structural conservation of base-pairing patterns and exceptional thermodynamic stability. We predict more than 30,000 structured RNA elements in the human genome, almost 1,000 of which are conserved across all vertebrates. Roughly a third are found in introns of known genes, a sixth are potential regulatory elements in untranslated regions of protein-coding mRNAs and about half are located far away from any known gene. Only a small fraction of these sequences has been described previously. A comparison with recent tiling array data shows that more than 40\\% of the predicted structured RNAs overlap with experimentally detected sites of transcription. The widespread conservation of secondary structure points to a large number of functional ncRNAs and cis-acting mRNA structures in the human genome. IS - 11 JF - Nat Biotechnol EP - 1390 TI - Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. VL - 23 SP - 1383 KW - acid KW - analysis KW - and KW - animals KW - base KW - biology KW - chromosome KW - computational KW - conformation KW - conserved KW - dna KW - elements KW - from_jabref KW - genetic KW - genome KW - govt KW - human KW - humans KW - introns KW - mapping KW - messenger KW - models KW - non-us KW - nucleic KW - pairing KW - phylogeny KW - regulatory KW - research KW - rna KW - sensitivity KW - sequence KW - specificity KW - statistical KW - support KW - thermodynamics KW - transcription KW - transcriptional KW - untranslated AU - Washietl, Stefan AU - Hofacker, Ivo AU - Lukasser, Melanie AU - Hüttenhofer, Alexander AU - Stadler, Peter PY - 2005/Nov// UR - http://dx.doi.org/10.1038/nbt1144 ER -