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  • *Evolution, Molecular  (1)
  • Histones/metabolism
  • American Association for the Advancement of Science (AAAS)  (1)
  • Nature Publishing Group (NPG)  (1)
  • 2010-2014  (2)
  • 1
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    A high-resolution map of human evolutionary constraint using 29 mammals (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-10-14
    Description: The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindblad-Toh, Kerstin -- Garber, Manuel -- Zuk, Or -- Lin, Michael F -- Parker, Brian J -- Washietl, Stefan -- Kheradpour, Pouya -- Ernst, Jason -- Jordan, Gregory -- Mauceli, Evan -- Ward, Lucas D -- Lowe, Craig B -- Holloway, Alisha K -- Clamp, Michele -- Gnerre, Sante -- Alfoldi, Jessica -- Beal, Kathryn -- Chang, Jean -- Clawson, Hiram -- Cuff, James -- Di Palma, Federica -- Fitzgerald, Stephen -- Flicek, Paul -- Guttman, Mitchell -- Hubisz, Melissa J -- Jaffe, David B -- Jungreis, Irwin -- Kent, W James -- Kostka, Dennis -- Lara, Marcia -- Martins, Andre L -- Massingham, Tim -- Moltke, Ida -- Raney, Brian J -- Rasmussen, Matthew D -- Robinson, Jim -- Stark, Alexander -- Vilella, Albert J -- Wen, Jiayu -- Xie, Xiaohui -- Zody, Michael C -- Broad Institute Sequencing Platform and Whole Genome Assembly Team -- Baldwin, Jen -- Bloom, Toby -- Chin, Chee Whye -- Heiman, Dave -- Nicol, Robert -- Nusbaum, Chad -- Young, Sarah -- Wilkinson, Jane -- Worley, Kim C -- Kovar, Christie L -- Muzny, Donna M -- Gibbs, Richard A -- Baylor College of Medicine Human Genome Sequencing Center Sequencing Team -- Cree, Andrew -- Dihn, Huyen H -- Fowler, Gerald -- Jhangiani, Shalili -- Joshi, Vandita -- Lee, Sandra -- Lewis, Lora R -- Nazareth, Lynne V -- Okwuonu, Geoffrey -- Santibanez, Jireh -- Warren, Wesley C -- Mardis, Elaine R -- Weinstock, George M -- Wilson, Richard K -- Genome Institute at Washington University -- Delehaunty, Kim -- Dooling, David -- Fronik, Catrina -- Fulton, Lucinda -- Fulton, Bob -- Graves, Tina -- Minx, Patrick -- Sodergren, Erica -- Birney, Ewan -- Margulies, Elliott H -- Herrero, Javier -- Green, Eric D -- Haussler, David -- Siepel, Adam -- Goldman, Nick -- Pollard, Katherine S -- Pedersen, Jakob S -- Lander, Eric S -- Kellis, Manolis -- 095908/Wellcome Trust/United Kingdom -- GM82901/GM/NIGMS NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-09/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA. kersli@broadinstitute.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993624" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Disease ; *Evolution, Molecular ; Exons/genetics ; Genome/*genetics ; Genome, Human/*genetics ; Genomics ; Health ; Humans ; Mammals/*genetics ; Molecular Sequence Annotation ; Phylogeny ; RNA/classification/genetics ; Selection, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Identification of functional elements and regulatory circuits by Drosophila modENCODE (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-12-24
    Description: To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉modENCODE Consortium -- Roy, Sushmita -- Ernst, Jason -- Kharchenko, Peter V -- Kheradpour, Pouya -- Negre, Nicolas -- Eaton, Matthew L -- Landolin, Jane M -- Bristow, Christopher A -- Ma, Lijia -- Lin, Michael F -- Washietl, Stefan -- Arshinoff, Bradley I -- Ay, Ferhat -- Meyer, Patrick E -- Robine, Nicolas -- Washington, Nicole L -- Di Stefano, Luisa -- Berezikov, Eugene -- Brown, Christopher D -- Candeias, Rogerio -- Carlson, Joseph W -- Carr, Adrian -- Jungreis, Irwin -- Marbach, Daniel -- Sealfon, Rachel -- Tolstorukov, Michael Y -- Will, Sebastian -- Alekseyenko, Artyom A -- Artieri, Carlo -- Booth, Benjamin W -- Brooks, Angela N -- Dai, Qi -- Davis, Carrie A -- Duff, Michael O -- Feng, Xin -- Gorchakov, Andrey A -- Gu, Tingting -- Henikoff, Jorja G -- Kapranov, Philipp -- Li, Renhua -- MacAlpine, Heather K -- Malone, John -- Minoda, Aki -- Nordman, Jared -- Okamura, Katsutomo -- Perry, Marc -- Powell, Sara K -- Riddle, Nicole C -- Sakai, Akiko -- Samsonova, Anastasia -- Sandler, Jeremy E -- Schwartz, Yuri B -- Sher, Noa -- Spokony, Rebecca -- Sturgill, David -- van Baren, Marijke -- Wan, Kenneth H -- Yang, Li -- Yu, Charles -- Feingold, Elise -- Good, Peter -- Guyer, Mark -- Lowdon, Rebecca -- Ahmad, Kami -- Andrews, Justen -- Berger, Bonnie -- Brenner, Steven E -- Brent, Michael R -- Cherbas, Lucy -- Elgin, Sarah C R -- Gingeras, Thomas R -- Grossman, Robert -- Hoskins, Roger A -- Kaufman, Thomas C -- Kent, William -- Kuroda, Mitzi I -- Orr-Weaver, Terry -- Perrimon, Norbert -- Pirrotta, Vincenzo -- Posakony, James W -- Ren, Bing -- Russell, Steven -- Cherbas, Peter -- Graveley, Brenton R -- Lewis, Suzanna -- Micklem, Gos -- Oliver, Brian -- Park, Peter J -- Celniker, Susan E -- Henikoff, Steven -- Karpen, Gary H -- Lai, Eric C -- MacAlpine, David M -- Stein, Lincoln D -- White, Kevin P -- Kellis, Manolis -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01HG004037/HG/NHGRI NIH HHS/ -- RC2HG005639/HG/NHGRI NIH HHS/ -- U01 HG004258/HG/NHGRI NIH HHS/ -- U01 HG004271/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004258/HG/NHGRI NIH HHS/ -- U01HG004261/HG/NHGRI NIH HHS/ -- U01HG004264/HG/NHGRI NIH HHS/ -- U01HG004271/HG/NHGRI NIH HHS/ -- U01HG004274/HG/NHGRI NIH HHS/ -- U01HG004279/HG/NHGRI NIH HHS/ -- U41HG004269/HG/NHGRI NIH HHS/ -- ZIA DK015600-14/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21177974" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; *Chromatin/genetics/metabolism ; Computational Biology/methods ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*genetics/growth & development/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation ; *Gene Regulatory Networks ; Genes, Insect ; *Genome, Insect ; Genomics/methods ; Histones/metabolism ; *Molecular Sequence Annotation ; Nucleosomes/genetics/metabolism ; Promoter Regions, Genetic ; RNA, Small Untranslated/genetics/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
    Location Call Number Expected Availability
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