Transcription factor binding variation in the evolution of gene regulation
Abstract
Transcription factor interactions with DNA are one of the primary mechanisms by which expression is modulated, yet their evolution remains poorly understood. Chromatin immunoprecipitation followed by microarray (ChIP-chip) or sequencing (ChIP-Seq) has revolutionized the study of protein-DNA interactions. However, only recently has attention focused on determining to what extent these regulatory interactions vary between species across entire genomes. A series of recent studies have compared in vivo binding data across a range of evolutionary distances. Binding events diverge rapidly, indicating gene regulation is an evolutionarily flexible process.
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Enhancer conservation is typically modular, commonly preserving the sets of binding sites for the required transcription factors, but often not their exact sequence and orientation.
“Instead, enhancer conservation is typically “modular”, commonly preserving the sets of binding sites for the required TFs, but often not their exact sequence and orientation [101–109].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [104]
Cites
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Tissue-specific transcriptional regulation has diverged significantly between human and mouse
Odom, D. T., Dowell, R. D., Jacobsen, E. S., Gordon, W., Danford, T. W., MacIsaac, K. D., Rolfe, P. A., Conboy, C. M., Gifford, D. K., & Fraenkel, E. (2007) · Nature Genetics · doi:10.1038/ng2047 · Cited by 506 · see citing works
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Serum response factor binding sites differ in three human cell types
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Cis-regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence
Wittkopp, P. J., & Kalay, G. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3095 · Cited by 1,231 · see citing works
YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
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Transcriptional enhancers and their communication with gene promoters
Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works
Functional characterization of enhancer evolution in the primate lineage
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- Authors
- Dowell, R. D.
- Affiliations
- University of Colorado Boulder (US)
- Corresponding author
- Dowell, Robin D.
- ORCID
- Dowell, Robin D.
- Venue
- Trends in Genetics
- Publisher
- Elsevier BV
- Published
- 2010-11
- Volume
- 26
- Issue
- 11
- Pages
- 468-475
- ISSN
- 0168-9525 (ISSN-L)
- OpenAlex
- W2007555386
- Cited by
- 61
- References
- 6
- Citations by year
- 2024: 2 · 2023: 2 · 2022: 2 · 2021: 1 · 2019: 2 · 2018: 3 · 2017: 4 · 2016: 1 · 2015: 6 · 2014: 11 · 2013: 5 · 2012: 13
- FWCI
- 0.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Trends in Genetics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- transcription factor binding, gene regulatory evolution, protein-DNA interactions, regulatory divergence, cross-species comparison, ChIP-chip, ChIP-seq
- MeSH terms
- Animals, Gene Expression Regulation, Humans, Transcription Factors, Sequence Analysis, DNA, Evolution, Molecular, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Chromatin Immunoprecipitation
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