Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.
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.
Denoeud
France
F
Grup de Recerca en Informática Biomèdica, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.
Kapranov
Philipp
P
Ucla
Catherine
C
Frankish
Adam
A
Castelo
Robert
R
Drenkow
Jorg
J
Lagarde
Julien
J
Alioto
Tyler
T
Manzano
Caroline
C
Chrast
Jacqueline
J
Dike
Sujit
S
Wyss
Carine
C
Henrichsen
Charlotte N
CN
Holroyd
Nancy
N
Dickson
Mark C
MC
Taylor
Ruth
R
Hance
Zahra
Z
Foissac
Sylvain
S
Myers
Richard M
RM
Rogers
Jane
J
Hubbard
Tim
T
Harrow
Jennifer
J
Guigó
Roderic
R
Gingeras
Thomas R
TR
Antonarakis
Stylianos E
SE
Reymond
Alexandre
A
D002874:Chromosome Mapping; D018076:DNA, Complementary / Q000235:genetics; D005091:Exons; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D016366:Open Reading Frames; D011401:Promoter Regions, Genetic; D040641:Quantitative Trait Loci; D014158:Transcription, Genetic / Q000502:physiology*
D018076:DNA, Complementary