ArticlePLoS computational biology2008
Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 25 citations in OpenAlex.
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- The effect of haplotypes in the promoter region of SIRT4 gene on the ultrasound traits in Qinchuan cattle.Tropical animal health and production · 2019Article
- Biophysical fitness landscapes for transcription factor binding sites.PLoS computational biology · 2014Article
- SNP variation in the promoter of the PRKAG3 gene and association with meat quality traits in pig.BMC genetics · 2012Article
- Article
- Evidence of association between nucleosome occupancy and the evolution of transcription factor binding sites in yeast.BMC evolutionary biology · 2011Article
- Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.Microbiology and molecular biology reviews : MMBR · 2009Review
- Different patterns of regulation for the copper and cadmium metallothioneins of the ectomycorrhizal fungus Hebeloma cylindrosporum.Applied and environmental microbiology · 2009Article
- Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.PLoS computational biology · 2009Article
- Evolution of regulatory sequences in 12 Drosophila species.PLoS genetics · 2009Article
- Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network.Nature biotechnology · 2008Article
- Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen Histoplasma capsulatum.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites.PLoS computational biology · 2008Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In comparative genomics one analyzes jointly evolutionarily related species in order to identify conserved and diverged sequences and to infer their function. While such studies enabled the detection of conserved sequences in large genomes, the evolutionary dynamics of regulatory regions as a whole remain poorly understood. Here we present a probabilistic model for the evolution of promoter regions in yeast, combining the effects of regulatory interactions of many different transcription factors. The model expresses explicitly the selection forces acting on transcription factor binding sites in the context of a dynamic evolutionary process. We develop algorithms to compute likelihood and to learn de novo collections of transcription factor binding motifs and their selection parameters from alignments. Using the new techniques, we examine the evolutionary dynamics in Saccharomyces species promoters. Analyses of an evolutionary model constructed using all known transcription factor binding motifs and of a model learned from the data automatically reveal relatively weak selection on most binding sites. Moreover, according to our estimates, strong binding sites are constraining only a fraction of the yeast promoter sequence that is under selection. Our study demonstrates how complex evolutionary dynamics in noncoding regions emerges from formalization of the evolutionary consequences of known regulatory mechanisms.
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