ArticleBMC evolutionary biology2009
Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.
Article in BMC evolutionary biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics.bioRxiv : the preprint server for biology · 2024Article
- Selection on the promoter regions plays an important role in complex traits during duck domestication.BMC biology · 2023Article
- Dynamic regulation of Monascus azaphilones biosynthesis by the binary MrPigE-MrPigF oxidoreductase system.Applied microbiology and biotechnology · 2022Article
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- Robust inference of positive selection on regulatory sequences in the human brain.Science advances · 2020Article
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- Decreased Transcription Factor Binding Levels Nearby Primate Pseudogenes Suggest Regulatory Degeneration.Molecular biology and evolution · 2016Article
- Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions.BMC evolutionary biology · 2016Article
- What does it take to evolve an enhancer? A simulation-based study of factors influencing the emergence of combinatorial regulation.Genome biology and evolution · 2015Article
- Cis-regulatory elements and human evolution.Current opinion in genetics & development · 2014Review
- Simulations of enhancer evolution provide mechanistic insights into gene regulation.Molecular biology and evolution · 2014Article
- A novel test for selection on cis-regulatory elements reveals positive and negative selection acting on mammalian transcriptional enhancers.Molecular biology and evolution · 2013Article
- Analysis of variation at transcription factor binding sites in Drosophila and humans.Genome biology · 2012Article
- Widespread site-dependent buffering of human regulatory polymorphism.PLoS genetics · 2012Article
- Methods to detect selection on noncoding DNA.Methods in molecular biology (Clifton, N.J.) · 2012Review
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- Article
- Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.PLoS genetics · 2011Article
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Abstract
backgroundAlthough cis-regulatory changes play an important role in evolution, it remains difficult to establish the contribution of natural selection to regulatory differences between species. For protein coding regions, powerful tests of natural selection have been developed based on comparisons of synonymous and non-synonymous substitutions, and analogous tests for regulatory regions would be of great utility.
resultsHere, tests for natural selection on regulatory regions are proposed based on nucleotide substitutions that occur in characterized transcription factor binding sites (an important type functional element within regulatory regions). In the absence of selection, these substitutions will tend to reduce the strength of existing binding sites. On the other hand, purifying selection will act to preserve the binding sites in regulatory regions, while positive selection can act to create or destroy binding sites, as well as change their strength. Using standard models of binding site strength and molecular evolution in the absence of selection, this intuition can be used to develop statistical tests for natural selection. Application of these tests to two well-characterized regulatory regions in Drosophila provides evidence for purifying selection.
conclusionThis demonstrates that it is possible to develop tests for selection on regulatory regions based on the specific functional constrains on these sequences.
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