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Structured RNAs in the ENCODE selected regions of the human genome

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dc.contributor.author Washietl, Stefan
dc.contributor.author Pedersen, Jackob S.
dc.contributor.author Korbel, Jan O.
dc.contributor.author Stocsits, Claudia
dc.contributor.author Gruber, Andreas R.
dc.contributor.author Hackermüller, Jörg
dc.contributor.author Hertel, Jana
dc.contributor.author Lindemeyer, Manja
dc.contributor.author Reiche, Kristin
dc.contributor.author Tanzer, Andrea
dc.contributor.author Ucla, Catherine
dc.contributor.author Wyss, Carine
dc.contributor.author Antonarakis, Stylianos E.
dc.contributor.author Denoeud, France
dc.contributor.author Lagarde, Julien
dc.contributor.author Drenkow, Jorg
dc.contributor.author Kapranov, Philipp
dc.contributor.author Gingeras, Thomas R.
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Snyder, Michael
dc.contributor.author Gerstein, Mark B.
dc.contributor.author Reymond, Alexandre
dc.contributor.author Hofacker, Ivo L.
dc.contributor.author Stadler, Peter F.
dc.date.accessioned 2012-05-21T09:45:01Z
dc.date.available 2012-05-21T09:45:01Z
dc.date.issued 2007
dc.identifier.citation Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007;17(6):852-64. DOI: 10.1101/gr.5650707
dc.identifier.issn 1088-9051
dc.identifier.uri http://hdl.handle.net/10230/16473
dc.description.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 ∼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 ∼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%).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Cold Spring Harbor Laboratory Press-CSHL Press
dc.relation.ispartof Genome Research. 2007;17(6):852-64
dc.rights © 2007 Genome Research by Cold Spring Harbor Laboratory Press. Published version available at http://genome.cshlp.org. Aquest document està subjecte a Llicència Creative Commons (Attribution-NonCommercial 3.0 Unported License)
dc.rights.uri http://creativecommons.org/licenses/by-nc/3.0/
dc.subject.other ARN
dc.subject.other Genètica humana
dc.title Structured RNAs in the ENCODE selected regions of the human genome
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1101/gr.5650707
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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