Coordinate enhancers share common organizational features in the Drosophila genome
Open accessAbstract
The evolution of animal diversity depends on changes in the regulation of a relatively fixed set of protein-coding genes. To understand how these changes might arise, we examined the organization of shared sequence motifs in four coordinately regulated neurogenic enhancers that direct similar patterns of gene expression in the early Drosophila embryo. All four enhancers possess similar arrangements of a subset of putative regulatory elements. These shared features were used to identify a neurogenic enhancer in the distantly related Anopheles genome. We suggest that the constrained organization of metazoan enhancers may be essential for their ability to produce precise patterns of gene expression during development. Organized binding sites should facilitate the identification of regulatory codes that link primary DNA sequence information with predicted patterns of gene activity.
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The organization of sites relative to each other, in particular the relationship between Dorsal and Twist transcription factors, may be important to support expression in given domains.
“Further analysis of cis-regulatory region architecture suggested that the organization of sites relative to each other, in particular of the relationship between Dorsal and Twist transcription factors, may be important to support expression in given domains”
From Graded dorsal and differential gene regulation in the Drosophila embryo. (2009) · cites this paper as Erives and Levine 2004
Cites
A CONSERVED SIGNALING PATHWAY: The <i>Drosophila</i> Toll-Dorsal Pathway
Belvin, M. P., & Anderson, K. V. (1996) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev.cellbio.12.1.393 · Cited by 836 · see citing works
A regulatory code for neurogenic gene expression in the<i>Drosophila</i>embryo
Markstein, M., Zinzen, R., Markstein, P., Yee, K.-P., Erives, A., Stathopoulos, A., & Levine, M. (2004) · Development · doi:10.1242/dev.01124 · Cited by 165 · see citing works
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Base-resolution models of transcription-factor binding reveal soft motif syntax
Avsec, Ž., Weilert, M., Shrikumar, A., Krueger, S., Alexandari, A., Dalal, K., Fropf, R., McAnany, C., Gagneur, J., Kundaje, A., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00782-6 · Cited by 610 · see citing works
Absence of a simple code: how transcription factors read the genome
Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537 · see citing works
Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?
Arnosti, D. N., & Kulkarni, M. M. (2005) · Journal of Cellular Biochemistry · doi:10.1002/jcb.20352 · Cited by 309 · see citing works
Graded dorsal and differential gene regulation in the Drosophila embryo.
Reeves, G. T., & Stathopoulos, A. (2009) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000836 · Cited by 119 · see citing works
Papatsenko, D., & Levine, M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409414102 · Cited by 82 · 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 · see citing works
Borok, M. J., Tran, D. A., Ho, M. C. W., & Drewell, R. A. (2010) · Development · doi:10.1242/dev.036160 · Cited by 54 · see citing works
- Authors
- Erives, A., & Levine, M.
- Affiliations
- University of California, Berkeley (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2004-03-16
- Volume
- 101
- Issue
- 11
- Pages
- 3851-3856
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC374333
- OpenAlex
- W2076313473
- Cited by
- 117
- References
- 2
- Citations by year
- 2024: 1 · 2023: 2 · 2022: 4 · 2021: 4 · 2020: 1 · 2019: 1 · 2018: 1 · 2016: 7 · 2015: 5 · 2014: 12 · 2013: 9 · 2012: 4
- FWCI
- 4.27
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5p01hd037105-20)
- National Institute of General Medical Sciences (R37GM046638, GM-46638, R01GM046638)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (P01-HD037105, P01 HD37105)
- 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
- Drosophila embryo, regulatory elements, transcription factor binding sites, developmental gene regulation, enhancer evolution
- MeSH terms
- Animals, Anopheles, Drosophila, Ectoderm, Enhancer Elements, Genetic, Transcription Factors, Sequence Analysis, DNA, Homeodomain Proteins, Computational Biology, Drosophila Proteins, Animals, Genetically Modified
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