ArticleGenome research2004
A global view of the selection forces in the evolution of yeast cis-regulation.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 30 citations in OpenAlex.
- Evolutionary dynamics of microRNA target sites across vertebrate evolution.PLoS genetics · 2020Article
- Computational identification of transcriptionally co-regulated genes, validation with the four ANT isoform genes.BMC genomics · 2012Article
- Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast.PloS one · 2012Article
- Article
- Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus.Molecular biology and evolution · 2011Article
- Tree-based position weight matrix approach to model transcription factor binding site profiles.PloS one · 2011Article
- Impact of DNA-binding position variants on yeast gene expression.Nucleic acids research · 2009Article
- CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.Genome biology · 2009Article
- Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network.Nature biotechnology · 2008Article
- Functional characterization of variations on regulatory motifs.PLoS genetics · 2008Article
- Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites.PLoS computational biology · 2008Article
- Coding limits on the number of transcription factors.BMC genomics · 2006Article
- Extensive low-affinity transcriptional interactions in the yeast genome.Genome research · 2006Article
- Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis.BMC bioinformatics · 2005Article
- Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence.Genome research · 2005Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The interaction between transcription factors and their DNA binding sites is key to understanding gene regulation. By performing a genome-wide study of the evolutionary dynamics in yeast promoters, we provide a first global view of the network of selection forces in the evolution of transcription factor binding sites. This analysis gives rise to new models for binding site activity, identifies families of related binding sites, and characterizes the functional similarities among them. We discovered rich and highly optimized selective pressures operating inside and around these families. In several cases, this organization reveals that a single transcription factor has multiple functional modes. We demonstrate how such functional heterogeneity is related to the binding site's affinity and how it is exploited in transcription programs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.