Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Export

@article{stark07, abstract = {Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.}, author = {Stark, A. and Lin, M. F. and Kheradpour, P. and Pedersen, J. S. and Parts, L. and Carlson, J. W. and Crosby, M. A. and Rasmussen, M. D. and Roy, S. and Deoras, A. N. and Ruby, J. G. and Brennecke, J. and {} and {} and Hodges, E. and Hinrichs, A. S. and Caspi, A. and Paten, B. and Park, S. W. and Han, M. V. and Maeder, M. L. and Polansky, B. J. and Robson, B. E. and Aerts, S. and van Helden, J. and Hassan, B. and Gilbert, D. G. and Eastman, D. A. and Rice, M. and Weir, M. and Hahn, M. W. and Park, Y. and Dewey, C. N. and Pachter, L. and Kent, W. J. and Haussler, D. and Lai, E. C. and Bartel, D. P. and Hannon, G. J. and Kaufman, T. C. and Eisen, M. B. and Clark, A. G. and Smith, D. and Celniker, S. E. and Gelbart, W. M. and Kellis, M.}, citeulike-article-id = {1880339}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature06340}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature06340}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17994088}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17994088}, day = {8}, doi = {10.1038/nature06340}, issn = {1476-4687}, journal = {Nature}, keywords = {12\_drosophila, gene\_regulation}, month = {November}, number = {7167}, pages = {219--232}, posted-at = {2009-03-26 15:51:31}, priority = {2}, publisher = {Nature Publishing Group}, title = {Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.}, url = {http://dx.doi.org/10.1038/nature06340}, volume = {450}, year = {2007} }

TY - JOUR ID - stark07 L3 - citeulike-article-id:1880339 N2 - Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies. IS - 7167 JF - Nature SN - 1476-4687 EP - 232 TI - Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. PB - Nature Publishing Group VL - 450 SP - 219 KW - 12_drosophila KW - gene_regulation AU - Stark, A AU - Lin, MF AU - Kheradpour, P AU - Pedersen, JS AU - Parts, L AU - Carlson, JW AU - Crosby, MA AU - Rasmussen, MD AU - Roy, S AU - Deoras, AN AU - Ruby, JG AU - Brennecke, J AU - Hodges, E AU - Hinrichs, AS AU - Caspi, A AU - Paten, B AU - Park, SW AU - Han, MV AU - Maeder, ML AU - Polansky, BJ AU - Robson, BE AU - Aerts, S AU - van Helden, J AU - Hassan, B AU - Gilbert, DG AU - Eastman, DA AU - Rice, M AU - Weir, M AU - Hahn, MW AU - Park, Y AU - Dewey, CN AU - Pachter, L AU - Kent, WJ AU - Haussler, D AU - Lai, EC AU - Bartel, DP AU - Hannon, GJ AU - Kaufman, TC AU - Eisen, MB AU - Clark, AG AU - Smith, D AU - Celniker, SE AU - Gelbart, WM AU - Kellis, M PY - 2007/11/08/ UR - http://dx.doi.org/10.1038/nature06340 ER -