Sat, 19 Jul 2008 11:25:59 BST CiteULike: xingxu's Cheng http://www.citeulike.org/user/xingxu/author/Cheng CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/xingxu/article/2311196 <i>European Journal of Human Genetics, Vol. aop, No. current.</i> 8q24 and prostate cancer: association with advanced disease and meta-analysis Iona Cheng Sarah Plummer Eric Jorgenson Xin Liu Benjamin Rybicki Graham Casey John Witte doi:10.1038/sj.ejhg.5201959 European Journal of Human Genetics, Vol. aop, No. current. 2008-01-31T11:58:13-00:00 European Journal of Human Genetics 1018-4813 aop current Nature Publishing Group 8q24 meta-analysis prostate review 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/1530903 <i>PLoS Genetics, Vol. 3, No. 7. (1 July 2007), e107.</i><br /><br />We describe here the Drosophila gene hydra that appears to have originated de novo in the melanogaster subgroup and subsequently evolved in both structure and expression level in Drosophila melanogaster and its sibling species. D. melanogaster hydra encodes a predicted protein of ~300 amino acids with no apparent similarity to any previously known proteins. The syntenic region flanking hydra on both sides is found in both D. ananassae and D. pseudoobscura, but hydra is found only in melanogaster subgroup species, suggesting that it originated less than ~13 million y ago. Exon 1 of hydra has undergone recurrent duplications, leading to the formation of nine tandem alternative exon 1s in D. melanogaster. Seven of these alternative exons are flanked on their 3′ side by the transposon DINE-1 (Drosophila interspersed element-1). We demonstrate that at least four of the nine duplicated exon 1s can function as alternative transcription start sites. The entire hydra locus has also duplicated in D. simulans and D. sechellia. D. melanogaster hydra is expressed most intensely in the proximal testis, suggesting a role in late-stage spermatogenesis. The coding region of hydra has a relatively high Ka/Ks ratio between species, but the ratio is less than 1 in all comparisons, suggesting that hydra is subject to functional constraint. Analysis of sequence polymorphism and divergence of hydra shows that it has evolved under positive selection in the lineage leading to D. melanogaster. The dramatic structural changes surrounding the first exons do not affect the tissue specificity of gene expression: hydra is expressed predominantly in the testes in D. melanogaster, D. simulans, and D. yakuba. However, we have found that expression level changed dramatically (~ >20-fold) between D. melanogaster and D. simulans. While hydra initially evolved in the absence of nearby transposable element insertions, we suggest that the subsequent accumulation of repetitive sequences in the hydra region may have contributed to structural and expression-level evolution by inducing rearrangements and causing local heterochromatinization. Our analysis further shows that recurrent evolution of both gene structure and expression level may be characteristics of newly evolved genes. We also suggest that late-stage spermatogenesis is the functional target for newly evolved and rapidly evolving male-specific genes. Evolution of hydra, a Recently Evolved Testis-Expressed Gene with Nine Alternative First Exons in Drosophila melanogaster Shou-Tao Chen Hsin-Chien Cheng Daniel Barbash Hsiao-Pei Yang doi:10.1371/journal.pgen.0030107 PLoS Genetics, Vol. 3, No. 7. (1 July 2007), e107. 2007-08-02T15:29:14-00:00 2007 PLoS Genetics 3 7 e107 drosophila evolution 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