Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.

By J. Zeitlinger, R. Zinzen, Alexander Stark, Manolis Kellis, Hailan Zhang, Richard A. Young, M. Levine. 2007

331 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm (2008, background): “The expression of many A-P genes is modulated up to 2-fold along the D-V axis [10,11] and analysis of genome-wide binding of the D-V factors Dorsal, Snail, Twist, Medea, and Zerknult show that these proteins bind to many A-P genes [38,39] (unpublished data).”
Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila (2014, background): “Transcription factors (TFs) are driven thermodynamically to bind to thousands of sites in genomic DNA, oftentimes nonspecifically (Lin and Riggs 1975; Walter et al. 1994; Phair et al. 2004; Elf et al. 2007; Zeitlinger et al. 2007; Li et al. 2008).”
Transcriptional enhancers: from properties to genome-wide predictions (2014, background): “For example, ChIP recovered essentially all previously known Twist-dependent mesodermal enhancers in D. melanogaster embryos 40,41 .”
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development (2011, methodology): “To map the occupancy patterns of specific regulators, chromatin immunoprecipitation (ChIP) has been applied to over 20 developmental transcription factors and RNA polymerase in the blastoderm embryo and, for several factors, at later stages of embryogenesis [30-36].”
Therapy for Fibrotic Diseases: Nearing the Starting Line (2013, background): “The transcriptional targets of Twist and Snail1 during development are well established (24), but it is not known whether these genes are relevant to fibrotic EMT.”
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007, background): “Similar results were found for motifs in known enhancers that were determined to be bound by ChIP (‘ChIP-bound’): 65% of Mef2 motifs, 65% of Snail motifs and 25% of Twist motifs were conserved (Fig.”
Zelda potentiates morphogen activity by increasing chromatin accessibility (2014, unknown): “5–3 hr embryos using amodified protocol from the Zeitlinger lab [45].”
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo (2007, methodology): “Previous studies have shown that the repression of a large set of genes in Toll 10b embryos depends on snail, a well-studied repressor that is constitutively expressed in Toll 10b embryos but not in Toll rm9/rm10 and gd 7 embryos 18,19,21–23 , 28 .”
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions (2009, background): “Several recent in vivo crosslinking studies have also noted significant overlap in binding between some sequence-specific factors in animals [32,34,37,44,46].”