UNIGE document Scientific Article
previous document  unige:8715  next document
add to browser collection

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

Denoeud, France
Kapranov, Philipp
Frankish, Adam
Castelo, Robert
Drenkow, Jorg
Lagarde, Julien
Alioto, Tyler
show hidden authors show all authors [1 - 26]
Published in Genome Research. 2007, vol. 17, no. 6, p. 746-759
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.
Keywords Chromosome MappingDNA, Complementary/geneticsExonsGenome, HumanHuman Genome ProjectHumansOpen Reading FramesPromoter Regions, GeneticQuantitative Trait LociTranscription, Genetic/ physiology
PMID: 17567994
Full text
Article - document accessible for UNIGE members only Limited access to UNIGE
Other version: http://genome.cshlp.org/content/17/6/746.full.pdf
(ISO format)
DENOEUD, France et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. In: Genome research, 2007, vol. 17, n° 6, p. 746-759. doi: 10.1101/gr.5660607 https://archive-ouverte.unige.ch/unige:8715

498 hits

0 download


Deposited on : 2010-07-12

Export document
Format :
Citation style :