Flexibility of transcription factor target site position in conserved cis-regulatory modules
Open accessAbstract
Eight Strongylocentrotus purpuratus cis-regulatory modules, in each of which up to three different transcription factor target sites had been previously authenticated in gene transfer and mutagenesis studies, were compared to the orthologous modules in the genome of Lytechinus variegatus. These species diverged about 50 million years ago. The orthologous modules were identified in sequenced Lytechinus BACs, as conserved sequence patches in similar regions of the respective genes. The similar functionality of several of these control modules in the two species was confirmed by cross-species gene transfer experiments. In each case the repertoire of transcription factor target sites was the same in the orthologous modules, but the positions of the individual sites with respect to one another was evolutionarily flexible, even though the intervening sequence was often strongly conserved. The most invariably conserved features, as seen also in other systems, were pairs of target sites that are immediately adjacent to one another. Their conservation is probably due to the necessity for interaction of proximally bound transcription factors, while a facilitated form of sequence conversion might be the mechanism of site position change.
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The arrangement, spacing, and number of target sites are relatively insignificant.
“The arrangement, spacing, and number of these sites is relatively insignificant (Balhoff and Wray, 2005; Cameron and Davidson, 2009; Dermitzakis et al., 2003; Liberman and Stathopoulos, 2009; Ludwig et al., 2000; Walters et al., 2008).”
From Evolution of Gene Regulatory Networks Controlling Body Plan Development (2011) · cites this paper as Cameron and Davidson, 2009
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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
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“Outside of the dipterans comparisons of orthologous CRMs have tended to focus on non-coding sequences a priori chosen for study because of their remarkable conservation, often extending from fish to mammals (Siepel et al., 2005; Vavouri et al., 2007; Elgar and Vavouri, 2008; Rastegar et al., 2008; Wang et al., 2009; P…”
Dermitzakis, E. T., & Clark, A. G. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004169 · Cited by 463 · see citing works
How the Dorsal gradient works: Insights from postgenome technologies
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Design flexibility in cis-regulatory control of gene expression: Synthetic and comparative evidence
Liberman, L. M., & Stathopoulos, A. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2008.12.020 · Cited by 76 · see citing works
Smith, J., & Davidson, E. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806442105 · Cited by 69 · see citing works
Self-citationHinman, V. F., Nguyen, A., & Davidson, E. H. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.09.006 · Cited by 67 · see citing works
Self-citationThe words of the regulatory code are arranged in a variable manner in highly conserved enhancers
Rastegar, S., Hess, I., Dickmeis, T., Nicod, J. C., Ertzer, R., Hadzhiev, Y., Thies, W.-G., Scherer, G., & Strähle, U. (2008) · Developmental Biology · doi:10.1016/j.ydbio.2008.03.034 · Cited by 56 · cited 4× · see citing works
“Outside of the dipterans comparisons of orthologous CRMs have tended to focus on non-coding sequences a priori chosen for study because of their remarkable conservation, often extending from fish to mammals (Siepel et al., 2005; Vavouri et al., 2007; Elgar and Vavouri, 2008; Rastegar et al., 2008; Wang et al., 2009; P…”
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Research works printed but not linked: 10
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Evolution of Gene Regulatory Networks Controlling Body Plan Development
Peter, I. S., & Davidson, E. H. (2011) · Cell · doi:10.1016/j.cell.2011.02.017 · Cited by 417 · see citing works
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- Authors
- Cameron, R. A., & Davidson, E. H.
- Affiliations
- California Institute of Technology (US)
- Corresponding author
- Cameron, R. Andrew
- ORCID
- Cameron, R. Andrew
- Venue
- Developmental Biology
- Publisher
- Elsevier BV
- Published
- 2009-12
- Volume
- 336
- Issue
- 1
- Pages
- 122-135
- ISSN
- 0012-1606 (ISSN-L)
- OpenAlex
- W2044542534
- Cited by
- 24
- References
- 7
- Citations by year
- 2026: 1 · 2025: 1 · 2021: 1 · 2019: 1 · 2018: 1 · 2017: 4 · 2016: 1 · 2015: 2 · 2014: 4 · 2013: 3 · 2012: 1
- FWCI
- 0.67
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Developmental Biology (publishedVersion)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- NSF (IOS-0517316)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- cis-regulatory modules, Strongylocentrotus purpuratus, Lytechinus variegatus, sea urchin genome, sequence conservation, transcription factor interaction, gene regulatory evolution
- MeSH terms
- Animals, Base Sequence, Binding Sites, Embryo, Nonmammalian, Microscopy, Fluorescence, Models, Genetic, Molecular Sequence Data, Regulatory Sequences, Nucleic Acid, Sequence Homology, Nucleic Acid, Transcription Factors, Conserved Sequence, Gene Expression Regulation, Developmental, Chromosomes, Artificial, Bacterial, Strongylocentrotus purpuratus, Lytechinus, Green Fluorescent Proteins
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