Structured RNAs in the ENCODE selected regions of the human genome.

Details

Serval ID
serval:BIB_0AC27ED2CF2C
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Structured RNAs in the ENCODE selected regions of the human genome.
Journal
Genome Research
Author(s)
Washietl S., Pedersen J.S., Korbel J.O., Stocsits C., Gruber A.R., Hackermüller J., Hertel J., Lindemeyer M., Reiche K., Tanzer A., Ucla C., Wyss C., Antonarakis S.E., Denoeud F., Lagarde J., Drenkow J., Kapranov P., Gingeras T.R., Guigó R., Snyder M., Gerstein M.B., Reymond A., Hofacker I.L., Stadler P.F.
ISSN
1088-9051[print], 1088-9051[linking]
Publication state
Published
Issued date
2007
Peer-reviewed
Oui
Volume
17
Number
6
Pages
852-864
Language
english
Abstract
Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic-stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding several thousand candidate structures (corresponding to approximately 2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3'-UTRs. While we estimate a significant false discovery rate of approximately 50%-70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz and EvoFold, and an additional 239 RNAz or EvoFold predictions are supported by the (more stringent) AlifoldZ algorithm. Five hundred seventy RNAz structure predictions fall into regions that show signs of selection pressure also on the sequence level (i.e., conserved elements). More than 700 predictions overlap with noncoding transcripts detected by oligonucleotide tiling arrays. One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%).
Keywords
3' Untranslated Regions/genetics, Base Sequence, GC Rich Sequence, Genome, Human, Humans, Molecular Sequence Data, Quantitative Trait Loci, RNA, Messenger/genetics, RNA, Untranslated/genetics, Reverse Transcriptase Polymerase Chain Reaction, Transcription, Genetic
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2008 15:52
Last modification date
20/08/2019 12:32
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