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Large-scale turnover of functional transcription factor binding sites in Drosophila

Moses, Alan M ; Pollard, Daniel A ; Nix, David A ; Iyer, Venky N ; Li, Xiao-Yong ; Biggin, Mark D ; Eisen, Michael B Sidow, Andrew

PLoS computational biology, 2006-10, Vol.2 (10), p.e130-e130 [Revista revisada por pares]

United States: Public Library of Science

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Título:
Large-scale turnover of functional transcription factor binding sites in Drosophila
Autor: Moses, Alan M ; Pollard, Daniel A ; Nix, David A ; Iyer, Venky N ; Li, Xiao-Yong ; Biggin, Mark D ; Eisen, Michael B
Sidow, Andrew
Materias: Animals ; Base Sequence ; Binding Sites ; Binding sites (Biochemistry) ; Bioinformatics - Computational Biology ; Computational Biology ; Conserved Sequence ; Deoxyribonucleic acid ; Development ; DNA ; DNA, Intergenic - genetics ; DNA-Binding Proteins - genetics ; Drosophila ; Drosophila melanogaster ; Drosophila melanogaster - genetics ; Drosophila melanogaster - metabolism ; Drosophila Proteins - genetics ; Drosophila simulans ; Evolution, Molecular ; Evolutionary biology ; Experiments ; Gene expression ; Genetic aspects ; Genetic transcription ; Genetics ; Genomes ; Insects ; Markov analysis ; Models, Genetic ; Molecular Sequence Data ; Phylogenetics ; Promoter Regions, Genetic - genetics ; Proteins ; Response Elements - genetics ; Selection, Genetic ; Sequence Alignment ; Systems Biology ; Transcription Factors - metabolism
Es parte de: PLoS computational biology, 2006-10, Vol.2 (10), p.e130-e130
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Descripción: The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an evolutionary model to study binding-site turnover that uses multiple sequence alignments to assess the evolutionary constraint on individual binding sites, and to map gain and loss events along a phylogenetic tree. We apply this model to study the evolutionary dynamics of binding sites of the Drosophila melanogaster transcription factor Zeste, using genome-wide in vivo (ChIP-chip) binding data to identify functional Zeste binding sites, and the genome sequences of D. melanogaster, D. simulans, D. erecta, and D. yakuba to study their evolution. We estimate that more than 5% of functional Zeste binding sites in D. melanogaster were gained along the D. melanogaster lineage or lost along one of the other lineages. We find that Zeste-bound regions have a reduced rate of binding-site loss and an increased rate of binding-site gain relative to flanking sequences. Finally, we show that binding-site gains and losses are asymmetrically distributed with respect to D. melanogaster, consistent with lineage-specific acquisition and loss of Zeste-responsive regulatory elements.
Editor: United States: Public Library of Science
Idioma: Inglés

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Large-scale turnover of functional transcription factor binding sites in Drosophila

Moses, Alan M ; Pollard, Daniel A ; Nix, David A ; Iyer, Venky N ; Li, Xiao-Yong ; Biggin, Mark D ; Eisen, Michael B Sidow, Andrew

United States: Public Library of Science

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