title: Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.
abstract: 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.
authors.affiliation: Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.
authors.forename: Julia
authors.initials: J
authors.lastname: Zeitlinger
authors.forename: Robert P
authors.initials: RP
authors.lastname: Zinzen
authors.forename: Alexander
authors.initials: A
authors.lastname: Stark
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: Hailan
authors.initials: H
authors.lastname: Zhang
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
authors.forename: Michael
authors.initials: M
authors.lastname: Levine
mesh_terms: D000818:Animals; D019521:Body Patterning / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D029721:Drosophila Proteins / Q000032:analysis / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000196:embryology* / Q000235:genetics; D004625:Embryo, Nonmammalian / Q000737:chemistry / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D018507:Gene Expression Regulation, Developmental; D049750:Genome, Insect / Q000235:genetics*; D009687:Nuclear Proteins / Q000032:analysis / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D010750:Phosphoproteins / Q000032:analysis / Q000378:metabolism*; D000071250:Snail Family Transcription Factors; D014157:Transcription Factors / Q000032:analysis / Q000378:metabolism*; D051879:Twist-Related Protein 1 / Q000032:analysis / Q000378:metabolism*
chemical_list: D029721:Drosophila Proteins; D009687:Nuclear Proteins; D010750:Phosphoproteins; D000071250:Snail Family Transcription Factors; D014157:Transcription Factors; C497753:Twi protein, Drosophila; D051879:Twist-Related Protein 1; C062236:dl protein, Drosophila; C000604451:sna protein, Drosophila