TY  - JOUR
A1  - Denoeud, France
A1  - Kapranov, Philipp
A1  - Ucla, Catherine
A1  - Frankish, Adam
A1  - Castelo, Robert
A1  - Drenkow, Jorg
A1  - Lagarde, Julien
A1  - Alioto, Tyler
A1  - Manzano, Caroline
A1  - Chrast, Jacqueline
A1  - Dike, Sujit
A1  - Wyss, Carine
A1  - Henrichsen, Charlotte N.
A1  - Holroyd, Nancy
A1  - Dickson, Mark C.
A1  - Taylor, Ruth
A1  - Hance, Zahra
A1  - Foissac, Sylvain
A1  - Myers, Richard M.
A1  - Rogers, Jane
A1  - Hubbard, Tim
A1  - Harrow, Jennifer
A1  - Guigó, Roderic
A1  - Gingeras, Thomas R.
A1  - Antonarakis, Stylianos E.
A1  - Reymond, Alexandre
T1  - Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
Y1  - 2007/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 746 
EP  - 759 
DO  - 10.1101/gr.5660607 
VL  - 17 
IS  - 6 
UR  - http://genome.cshlp.org/content/17/6/746.abstract 
N2  - 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. 
ER  -