Comparative analyses of multi-species sequences from targeted genomic regions Export

@article{citeulike:276972, abstract = {The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.}, address = {Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892,USA.}, author = {Thomas, J. W. and Touchman, J. W. and Blakesley, R. W. and Bouffard, G. G. and Beckstrom-Sternberg, S. M. and Margulies, E. H. and Blanchette, M. and Siepel, A. C. and Thomas, P. J. and Mcdowell, J. C. and Maskeri, B. and Hansen, N. F. and Schwartz, M. S. and Weber, R. J. and Kent, W. J. and Karolchik, D. and Bruen, T. C. and Bevan, R. and Cutler, D. J. and Schwartz, S. and Elnitski, L. and Idol, J. R. and Prasad, A. B. and Lee-Lin, S. Q. and Maduro, V. V. B. and Summers, T. J. and Portnoy, M. E. and Dietrich, N. L. and Akhter, N. and Ayele, K. and Benjamin, B. and Cariaga, K. and Brinkley, C. P. and Brooks, S. Y. and Granite, S. and Guan, X. and Gupta, J. and Haghighi, P. and Ho, S. L. and Huang, M. C. and Karlins, E. and Laric, P. L. and Legaspi, R. and Lim, M. J. and Maduro, Q. L. and Masiello, C. A. and Mastrian, S. D. and Mccloskey, J. C. and Pearson, R. and Stantripop, S. and Tiongson, E. E. and Tran, J. T. and Tsurgeon, C. and Vogt, J. L. and Walker, M. A. and Wetherby, K. D. and Wiggins, L. S. and Young, A. C. and Zhang, L. H. and Osoegawa, K. and Zhu, B. and Zhao, B. and Shu, C. L. and De Jong, P. J. and Lawrence, C. E. and Smit, A. F. and Chakravarti, A. and Haussler, D. and Green, P. and Miller, W. and Green, E. D.}, citeulike-article-id = {276972}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature01858}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature01858}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/12917688}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=12917688}, day = {14}, doi = {10.1038/nature01858}, issn = {1476-4687}, journal = {Nature}, keywords = {comparative, empirical, evolution, selection, species}, month = {August}, number = {6950}, pages = {788--793}, posted-at = {2009-03-25 15:18:07}, priority = {2}, title = {Comparative analyses of multi-species sequences from targeted genomic regions}, url = {http://dx.doi.org/10.1038/nature01858}, volume = {424}, year = {2003} }

TY - JOUR ID - citeulike:276972 L3 - citeulike-article-id:276972 N2 - The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates. IS - 6950 JF - Nature SN - 1476-4687 AD - Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892,USA. EP - 793 TI - Comparative analyses of multi-species sequences from targeted genomic regions VL - 424 SP - 788 KW - comparative KW - empirical KW - evolution KW - selection KW - species AU - Thomas, JW AU - Touchman, JW AU - Blakesley, RW AU - Bouffard, GG AU - Beckstrom-Sternberg, SM AU - Margulies, EH AU - Blanchette, M AU - Siepel, AC AU - Thomas, PJ AU - Mcdowell, JC AU - Maskeri, B AU - Hansen, NF AU - Schwartz, MS AU - Weber, RJ AU - Kent, WJ AU - Karolchik, D AU - Bruen, TC AU - Bevan, R AU - Cutler, DJ AU - Schwartz, S AU - Elnitski, L AU - Idol, JR AU - Prasad, AB AU - Lee-Lin, SQ AU - Maduro, VVB AU - Summers, TJ AU - Portnoy, ME AU - Dietrich, NL AU - Akhter, N AU - Ayele, K AU - Benjamin, B AU - Cariaga, K AU - Brinkley, CP AU - Brooks, SY AU - Granite, S AU - Guan, X AU - Gupta, J AU - Haghighi, P AU - Ho, SL AU - Huang, MC AU - Karlins, E AU - Laric, PL AU - Legaspi, R AU - Lim, MJ AU - Maduro, QL AU - Masiello, CA AU - Mastrian, SD AU - Mccloskey, JC AU - Pearson, R AU - Stantripop, S AU - Tiongson, EE AU - Tran, JT AU - Tsurgeon, C AU - Vogt, JL AU - Walker, MA AU - Wetherby, KD AU - Wiggins, LS AU - Young, AC AU - Zhang, LH AU - Osoegawa, K AU - Zhu, B AU - Zhao, B AU - Shu, CL AU - De Jong, PJ AU - Lawrence, CE AU - Smit, AF AU - Chakravarti, A AU - Haussler, D AU - Green, P AU - Miller, W AU - Green, ED PY - 2003/08/14/ UR - http://dx.doi.org/10.1038/nature01858 ER -