Welcome to the UPF Digital Repository

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution

Show simple item record

dc.contributor.author Zheng, Deyou
dc.contributor.author Frankish, Adam
dc.contributor.author Baertsch, Robert
dc.contributor.author Kapranov, Philipp
dc.contributor.author Reymond, Alexandre
dc.contributor.author Choo, Siew Woh
dc.contributor.author Lu, Yontao
dc.contributor.author Denoeud, France
dc.contributor.author Antonarakis, Stylianos E.
dc.contributor.author Snyder, Michael
dc.contributor.author Ruan, Yijun
dc.contributor.author Wei, Chia-Lin
dc.contributor.author Gingeras, Thomas R.
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Harrow, Jennifer
dc.contributor.author Gerstein, Mark B.
dc.date.accessioned 2012-05-21T09:44:59Z
dc.date.available 2012-05-21T09:44:59Z
dc.date.issued 2007
dc.identifier.citation Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res. 2007;17(6):839-51. DOI: 10.1101/gr.5586307
dc.identifier.issn 1088-9051
dc.identifier.uri http://hdl.handle.net/10230/16472
dc.description.abstract Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome’s structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction (∼80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.
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):839-51
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 Genètica evolutiva
dc.subject.other Factors de transcripció
dc.title Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1101/gr.5586307
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


This item appears in the following Collection(s)

Show simple item record

Search DSpace

Advanced Search


My Account


In collaboration with Compliant to Partaking