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A high-resolution map of human evolutionary constraint using 29 mammals.

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Date
2011-10-12
Authors
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
Alföldi, 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
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Abstract
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 ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼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.
Type
Journal article
Subject
Broad Institute Sequencing Platform and Whole Genome Assembly Team
Baylor College of Medicine Human Genome Sequencing Center Sequencing Team
Genome Institute at Washington University
Animals
Mammals
Humans
Disease
RNA
Sequence Alignment
Sequence Analysis, DNA
Genomics
Evolution, Molecular
Phylogeny
Genome
Genome, Human
Exons
Health
Selection, Genetic
Molecular Sequence Annotation
Permalink
https://hdl.handle.net/10161/17408
Published Version (Please cite this version)
10.1038/nature10530
Publication Info
Lindblad-Toh, Kerstin; Garber, Manuel; Zuk, Or; Lin, Michael F; Parker, Brian J; Washietl, Stefan; ... Kellis, Manolis (2011). A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478(7370). pp. 476-482. 10.1038/nature10530. Retrieved from https://hdl.handle.net/10161/17408.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Scholars@Duke

Lowe

Craig Lowe

Assistant Professor of Molecular Genetics and Microbiology
Open Access

Articles written by Duke faculty are made available through the campus open access policy. For more information see: Duke Open Access Policy

Rights for Collection: Scholarly Articles

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