ArticleMolecular systems biology2008
On the relation between promoter divergence and gene expression evolution.
Article in Molecular systems biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 86 citations in OpenAlex.
- Using knowledge graphs to infer gene expression in plants.Frontiers in artificial intelligence · 2023Article
- Article
- Genome-wide analysis of yeast expression data based on a priori generated co-regulation cliques.Microbial cell (Graz, Austria) · 2019Article
- Sequence and functional characterization of MIRNA164 promoters from Brassica shows copy number dependent regulatory diversification among homeologs.Functional & integrative genomics · 2018Article
- Article
- Cis-Regulatory Divergence in Gene Expression between Two Thermally Divergent Yeast Species.Genome biology and evolution · 2017Article
- Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression.Molecular biology and evolution · 2016Article
- Construction and evaluation of yeast expression networks by database-guided predictions.Microbial cell (Graz, Austria) · 2016Article
- Combinatorial Cis-regulation in Saccharomyces Species.G3 (Bethesda, Md.) · 2016Article
- Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus.Genome biology and evolution · 2015Article
- Article
- Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.Genome research · 2015Article
- Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters.Genome research · 2014Article
- Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.PLoS computational biology · 2014Article
- A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators.Genome biology · 2014Article
- Biophysical fitness landscapes for transcription factor binding sites.PLoS computational biology · 2014Article
- Pervasive divergence of transcriptional gene regulation in Caenorhabditis nematodes.PLoS genetics · 2014Article
- Comparative gene expression between two yeast species.BMC genomics · 2013Article
- Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.PLoS genetics · 2013Article
- The relationship between gene isoform multiplicity, number of exons and protein divergence.PloS one · 2013Article
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Authors and funding
5 authors at 1 institution in 1 country.
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Abstract
Recent studies have characterized significant differences in the cis-regulatory sequences of related organisms, but the impact of these differences on gene expression remains largely unexplored. Here, we show that most previously identified differences in transcription factor (TF)-binding sequences of yeasts and mammals have no detectable effect on gene expression, suggesting that compensatory mechanisms allow promoters to rapidly evolve while maintaining a stabilized expression pattern. To examine the impact of changes in cis-regulatory elements in a more controlled setting, we compared the genes induced during mating of three yeast species. This response is governed by a single TF (STE12), and variations in its predicted binding sites can indeed account for about half of the observed expression differences. The remaining unexplained differences are correlated with the increased divergence of the sequences that flank the binding sites and an apparent modulation of chromatin structure. Our analysis emphasizes the flexibility of promoter structure, and highlights the interplay between specific binding sites and general chromatin structure in the control of gene expression.
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