Sat, 26 Jul 2008 08:06:54 BST CiteULike: xingxu's Kapranov http://www.citeulike.org/user/xingxu/author/Kapranov CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/xingxu/article/1336057 <i>Science (17 May 2007), 1138341.</i><br /><br />Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the relations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides and whole-cell RNAs less than 200 nt are investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three novel potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome. 10.1126/science.1138341 RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription Philipp Kapranov Jill Cheng Sujit Dike David Nix Radharani Duttagupta Aarron Willingham Peter Stadler Jana Hertel Joerg Hackermueller Ivo Hofacker Ian Bell Evelyn Cheung Jorg Drenkow Erica Dumais Sandeep Patel Gregg Helt Madhavan Ganesh Srinka Ghosh Antonio Piccolboni Victor Sementchenko Hari Tammana Thomas Gingeras doi:10.1126/science.1138341 Science (17 May 2007), 1138341. 2007-05-27T00:42:53-00:00 2007 Science 1138341 breakthrough methods transcriptome http://www.citeulike.org/user/xingxu/article/876191 <i>Nature Genetics, Vol. 38, No. 10. (03 September 2006), pp. 1151-1158.</i> Biological function of unannotated transcription during the early development of Drosophila melanogaster Robert Manak Sujit Dike Victor Sementchenko Philipp Kapranov Frederic Biemar Jeff Long Jill Cheng Ian Bell Srinka Ghosh Antonio Piccolboni Thomas Gingeras doi:10.1038/ng1875 Nature Genetics, Vol. 38, No. 10. (03 September 2006), pp. 1151-1158. 2006-09-28T09:22:15-00:00 2006 Nature Genetics 1061-4036 38 10 1151 1158 Nature Publishing Group affymetrix drosophila genomics race http://www.citeulike.org/user/xingxu/article/1388730 <i>Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 746-759.</i><br /><br />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. 10.1101/gr.5660607 Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions France Denoeud Philipp Kapranov Catherine Ucla Adam Frankish Robert Castelo Jorg Drenkow Julien Lagarde Tyler Alioto Caroline Manzano Jacqueline Chrast Sujit Dike Carine Wyss Charlotte Henrichsen Nancy Holroyd Mark Dickson Ruth Taylor Zahra Hance Sylvain Foissac Richard Myers Jane Rogers Tim Hubbard Jennifer Harrow Roderic Guigo Thomas Gingeras Stylianos Antonarakis Alexandre Reymond doi:10.1101/gr.5660607 Genome Res., Vol. 17, No. 6. (1 June 2007), pp. 746-759. 2007-06-14T00:04:11-00:00 2007 Genome Res. 17 6 746 759 encode genomics race