Whole-genome ChIP–chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
Open accessAbstract
Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determined the genome-wide occupancy of the dorsoventral (DV) determinants Dorsal, Twist, and Snail in the Drosophila embryo using chromatin immunoprecipitation coupled with microarray analysis (ChIP–chip). The in vivo binding of these proteins correlate tightly with the limits of known enhancers. Our analysis predicts substantially more target genes than previous estimates, and includes Dpp signaling components and anteroposterior (AP) segmentation determinants. Thus, the ChIP–chip data uncover a much larger than expected regulatory network, which integrates diverse patterning processes during development.
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Five novel Dorsal-binding and six novel Twist-binding cis-regulatory sequences were confirmed.
“Five novel Dorsal-binding (Zeitlinger et al. 2007) and six novel Twistbinding cis-regulatory sequences (Sandmann et al. 2007) were confirmed.”
From Graded dorsal and differential gene regulation in the Drosophila embryo. (2009) · cites this paper as Zeitlinger et al. 2007
ChIP-chip methodology identified in vivo binding site occupancy for Dorsal, Twist, and Snail transcription factors.
“Experiments to identify cis-regulatory regions using ChIP-chip methodology were able to identify in vivo binding site occupancy for Dorsal, Twist, and Snail transcription factors”
From Graded dorsal and differential gene regulation in the Drosophila embryo. (2009) · cites this paper as Zeitlinger et al. 2007
These studies suggested extensive cross talk between dorsoventral and anteroposterior patterning.
“These studies also suggested extensive cross talk between DV and AP patterning”
From Graded dorsal and differential gene regulation in the Drosophila embryo. (2009) · cites this paper as Zeitlinger et al. 2007
ChIP-chip analyses with Dorsal, Snail, and Twist antibodies reveal strong binding peaks for one or more of these proteins in several AP patterning genes.
“ChIP-chip analyses with Dorsal, Snail, and Twist antibodies reveal strong binding peaks (left) for one or more of these proteins in several AP patterning genes.”
From Graded dorsal and differential gene regulation in the Drosophila embryo. (2009) · cites this paper as Zeitlinger et al. 2007
ChIP-chip studies have uncovered multiple enhancer sites and cross talk between AP and DV systems.
“ChIP-chip studies have uncovered multiple enhancer sites and cross talk between AP and DV systems.”
From Graded dorsal and differential gene regulation in the Drosophila embryo. (2009) · cites this paper as Zeitlinger et al. 2007
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- Authors
- Zeitlinger, J., Zinzen, R. P., Stark, A., Kellis, M., Zhang, H., Young, R. A., & Levine, M.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- University of California, Berkeley (US)
- Broad Institute (US)
- Icahn School of Medicine at Mount Sinai (US)
- ORCID
- Venue
- Genes & Development
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2007-02-15
- Volume
- 21
- Issue
- 4
- Pages
- 385-390
- ISSN
- 0890-9369 (ISSN-L)
- 1549-5477
- PMC
- PMC1804326
- OpenAlex
- W2122535550
- Cited by
- 286
- References
- 3
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 7 · 2023: 7 · 2022: 4 · 2021: 10 · 2020: 4 · 2019: 12 · 2018: 13 · 2017: 7 · 2016: 18 · 2015: 16 · 2014: 20 · 2013: 18 · 2012: 27
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genes & Development (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Gordon and Betty Moore Foundation
- National Institutes of Health (GM 46638)
- National Human Genome Research Institute (HG02668, R01HG002668, R01HG004037)
- National Institute of General Medical Sciences (R37GM046638, GM 069676, GM-46638, R01GM046638, R01GM069676)
- 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 › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- Dorsal, Twist, snails, dorsoventral patterning, Drosophila embryo, transcription factor binding sites, enhancers, target genes, Dpp signaling, developmental patterning, transcriptional regulatory networks
- MeSH terms
- Snail Family Transcription Factors, Animals, Drosophila melanogaster, Embryo, Nonmammalian, Enhancer Elements, Genetic, Nuclear Proteins, Phosphoproteins, Transcription Factors, Gene Expression Regulation, Developmental, Body Patterning, Oligonucleotide Array Sequence Analysis, Drosophila Proteins, Chromatin Immunoprecipitation, Genome, Insect, Twist-Related Protein 1
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