Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

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Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007; 17(6): 746-59. DOI: 10.1101/gr.5660607
http://hdl.handle.net/10230/16477
To cite or link this document: http://hdl.handle.net/10230/16477
dc.contributor.author Denoeud, France
dc.contributor.author Kapranov, Philipp
dc.contributor.author Ucla, Catherine
dc.contributor.author Frankish, Adam
dc.contributor.author Castelo, Robert
dc.contributor.author Drenkow, Jorg
dc.contributor.author Lagarde, Julien
dc.contributor.author Alioto, Tyler
dc.contributor.author Manzano, Caroline
dc.contributor.author Chrast, Jacqueline
dc.contributor.author Dike, Sujit
dc.contributor.author Wyss, Carine
dc.contributor.author Henrichsen, Charlotte N.
dc.contributor.author Holroyd, Nancy
dc.contributor.author Dickson, Mark C.
dc.contributor.author Taylor, Ruth
dc.contributor.author Hance, Zahra
dc.contributor.author Foissac, Sylvain
dc.contributor.author Myers, Richard M.
dc.contributor.author Rogers, Jane
dc.contributor.author Hubbard, Tim
dc.contributor.author Harrow, Jennifer
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Gingeras, Thomas R.
dc.contributor.author Antonarakis, Stylianos E.
dc.contributor.author Reymond, Alexandre
dc.date.accessioned 2012-05-21T09:45:08Z
dc.date.available 2012-05-21T09:45:08Z
dc.date.issued 2007
dc.identifier.citation Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007; 17(6): 746-59. DOI: 10.1101/gr.5660607
dc.identifier.issn 1088-9051
dc.identifier.uri http://hdl.handle.net/10230/16477
dc.description.abstract This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.
dc.language.iso eng
dc.publisher Cold Spring Harbor Laboratory Press-CSHL Press
dc.relation.ispartof Genome Res. 2007; 17(6): 746-59
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 Factors de transcripció
dc.subject.other Genoma humà
dc.title Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1101/gr.5660607
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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