ArticlePLoS genetics2009
Evolution of regulatory sequences in 12 Drosophila species.
Article in PLoS genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- A transcriptomic atlas of acute stress response to low pH in multipleMicrobiology spectrum · 2024Article
- Homology of process: developmental dynamics in comparative biology.Interface focus · 2021Article
- A phylogeny for the Drosophila montium species group: A model clade for comparative analyses.Molecular phylogenetics and evolution · 2021Article
- Adaptive gene misregulation.Genetics · 2021Article
- Whole Genome Sequences of 23 Species from theG3 (Bethesda, Md.) · 2020Article
- Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.Nucleic acids research · 2020Article
- Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana.Molecular biology and evolution · 2018Article
- Insect antimicrobial peptides act synergistically to inhibit a trypanosome parasite.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Article
- Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution.PLoS genetics · 2016Article
- Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression.Molecular biology and evolution · 2016Article
- Evolutionary Footprints of Short Tandem Repeats in Avian Promoters.Scientific reports · 2016Article
- A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity.PLoS genetics · 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
- Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila.BMC genomics · 2015Article
- Pervasive variation of transcription factor orthologs contributes to regulatory network evolution.PLoS genetics · 2015Article
- Article
- Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.PLoS computational biology · 2014Article
- Spurious transcription factor binding: non-functional or genetically redundant?BioEssays : news and reviews in molecular, cellular and developmental biology · 2014Article
- Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change.Molecular biology and evolution · 2014Article
- Evolution of transcription factor binding in metazoans - mechanisms and functional implications.Nature reviews. Genetics · 2014Review
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Characterization of the evolutionary constraints acting on cis-regulatory sequences is crucial to comparative genomics and provides key insights on the evolution of organismal diversity. We study the relationships among orthologous cis-regulatory modules (CRMs) in 12 Drosophila species, especially with respect to the evolution of transcription factor binding sites, and report statistical evidence in favor of key evolutionary hypotheses. Binding sites are found to have position-specific substitution rates. However, the selective forces at different positions of a site do not act independently, and the evidence suggests that constraints on sites are often based on their exact binding affinities. Binding site loss is seen to conform to a molecular clock hypothesis. The rate of site loss is transcription factor-specific and depends on the strength of binding and, in some cases, the presence of other binding sites in close proximity. Our analysis is based on a novel computational method for aligning orthologous CRMs on a tree, which rigorously accounts for alignment uncertainties and exploits binding site predictions through a unified probabilistic framework. Finally, we report weak purifying selection on short deletions, providing important clues about overall spatial constraints on CRMs. Our results present a complex picture of regulatory sequence evolution, with substantial plasticity that depends on a number of factors. The insights gained in this study will help us to understand the combinatorial control of gene regulation and how it evolves. They will pave the way for theoretical models that are cognizant of the important determinants of regulatory sequence evolution and will be critical in genome-wide identification of non-coding sequences under purifying or positive selection.
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