ArticleGenome biology and evolution2010
Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?
Article in Genome biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 25 citations in OpenAlex.
- Evolution of transcription factor binding through sequence variations and turnover of binding sites.Genome research · 2022Article
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- Co-opted transposons help perpetuate conserved higher-order chromosomal structures.Genome biology · 2020Article
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- Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals.PLoS computational biology · 2018Article
- Single-Base Resolution Map of Evolutionary Constraints and Annotation of Conserved Elements across Major Grass Genomes.Genome biology and evolution · 2018Article
- Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences.Nucleic acids research · 2017Article
- Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression.Molecular biology and evolution · 2016Article
- BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.Bioinformatics (Oxford, England) · 2015Article
- Pervasive variation of transcription factor orthologs contributes to regulatory network evolution.PLoS genetics · 2015Article
- Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns.PloS one · 2014Article
- A geometric interpretation for local alignment-free sequence comparison.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.Frontiers in plant science · 2013Article
- Article
- The population genetics of cooperative gene regulation.BMC evolutionary biology · 2012Article
- A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains.Nucleic acids research · 2012Article
- Stochastic signalling rewires the interaction map of a multiple feedback network during yeast evolution.Nature communications · 2012Article
- Positive evolutionary selection of an HD motif on Alzheimer precursor protein orthologues suggests a functional role.PLoS computational biology · 2012Article
- Divergence of the yeast transcription factor FZF1 affects sulfite resistance.PLoS genetics · 2012Article
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2 authors at 1 institution in 1 country.
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Abstract
The molecular evolution of cis-regulatory sequences is not well understood. Comparisons of closely related species show that cis-regulatory sequences contain a large number of sites constrained by purifying selection. In contrast, there are a number of examples from distantly related species where cis-regulatory sequences retain little to no sequence similarity but drive similar patterns of gene expression. Binding site turnover, whereby the gain of a redundant binding site enables loss of a previously functional site, is one model by which cis-regulatory sequences can diverge without a concurrent change in function. To determine whether cis-regulatory sequence divergence is consistent with binding site turnover, we examined binding site evolution within orthologous intergenic sequences from 14 yeast species defined by their syntenic relationships with adjacent coding sequences. Both local and global alignments show that nearly all distantly related orthologous cis-regulatory sequences have no significant level of sequence similarity but are enriched for experimentally identified binding sites. Yet, a significant proportion of experimentally identified binding sites that are conserved in closely related species are absent in distantly related species and so cannot be explained by binding site turnover. Depletion of binding sites depends on the transcription factor but is detectable for a quarter of all transcription factors examined. Our results imply that binding site turnover is not a sufficient explanation for cis-regulatory sequence evolution.
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