title: Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.
abstract: Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. We used whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over 40 well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
authors.forename: Xiao-yong
authors.initials: XY
authors.lastname: Li
authors.forename: Stewart
authors.initials: S
authors.lastname: MacArthur
authors.forename: Richard
authors.initials: R
authors.lastname: Bourgon
authors.forename: David
authors.initials: D
authors.lastname: Nix
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Pollard
authors.forename: Venky N
authors.initials: VN
authors.lastname: Iyer
authors.forename: Aaron
authors.initials: A
authors.lastname: Hechmer
authors.forename: Lisa
authors.initials: L
authors.lastname: Simirenko
authors.forename: Mark
authors.initials: M
authors.lastname: Stapleton
authors.forename: Cris L
authors.initials: CL
authors.lastname: Luengo Hendriks
authors.forename: Hou Cheng
authors.initials: HC
authors.lastname: Chu
authors.forename: Nobuo
authors.initials: N
authors.lastname: Ogawa
authors.forename: William
authors.initials: W
authors.lastname: Inwood
authors.forename: Victor
authors.initials: V
authors.lastname: Sementchenko
authors.forename: Amy
authors.initials: A
authors.lastname: Beaton
authors.forename: Richard
authors.initials: R
authors.lastname: Weiszmann
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.forename: David W
authors.initials: DW
authors.lastname: Knowles
authors.forename: Tom
authors.initials: T
authors.lastname: Gingeras
authors.forename: Terence P
authors.initials: TP
authors.lastname: Speed
authors.forename: Michael B
authors.initials: MB
authors.lastname: Eisen
authors.forename: Mark D
authors.initials: MD
authors.lastname: Biggin
mesh_terms: D000818:Animals; D001665:Binding Sites; D001756:Blastoderm / Q000378:metabolism*; D004247:DNA / Q000378:metabolism; D004331:Drosophila melanogaster / Q000196:embryology*; D019143:Evolution, Molecular; D035683:MicroRNAs / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors; D004247:DNA