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- Title
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.
- Authors
Washietl, Stefan; Hofacker, Ivo L; Lukasser, Melanie; Hüttenhofer, Alexander; Stadler, Peter F
- 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.
- Publication
Nature biotechnology, 2005, Vol 23, Issue 11, p1383
- ISSN
1087-0156
- Publication type
Journal Article
- DOI
10.1038/nbt1144