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

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• dc.contributor.author Zheng, Deyouca
• dc.contributor.author Frankish, Adamca
• dc.contributor.author Baertsch, Robertca
• dc.contributor.author Kapranov, Philippca
• dc.contributor.author Reymond, Alexandreca
• dc.contributor.author Choo, Siew Wohca
• dc.contributor.author Lu, Yontaoca
• dc.contributor.author Denoeud, Franceca
• dc.contributor.author Antonarakis, Stylianos E.ca
• dc.contributor.author Snyder, Michaelca
• dc.contributor.author Ruan, Yijunca
• dc.contributor.author Wei, Chia-Linca
• dc.contributor.author Gingeras, Thomas R.ca
• dc.contributor.author Guigó Serra, Rodericca
• dc.contributor.author Harrow, Jenniferca
• dc.contributor.author Gerstein, Mark B.ca
• dc.date.accessioned 2012-05-21T09:44:59Z
• dc.date.available 2012-05-21T09:44:59Z
• dc.date.issued 2007ca
• 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/pdfca
• 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.5586307ca
• dc.identifier.doi http://dx.doi.org/10.1101/gr.5586307
• dc.identifier.issn 1088-9051ca
• dc.identifier.uri http://hdl.handle.net/10230/16472
• dc.language.iso engca
• dc.publisher Cold Spring Harbor Laboratory Press-CSHL Pressca
• 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)ca
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• 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 evolutionca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersion