title: Spatial expression of transcription factors in Drosophila embryonic organ development.
abstract: BACKGROUND
  Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown.
  
  
  RESULTS
  We present a systematic characterization of spatiotemporal gene expression patterns for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary, and analyzed TF expression in the context of organ system development. Nearly all TFs are expressed during embryogenesis and more than half are specifically expressed in the central nervous system. Compared to other genes, TFs are enriched early in the development of most organ systems, and throughout the development of the nervous system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed in multiple organ systems while 21% show single-organ specificity. Of those expressed in multiple organ systems, 77 TFs are restricted to a single organ system either early or late in development. Expression patterns for 354 TFs are characterized for the first time in this study.
  
  
  CONCLUSIONS
  We produced a reference TF dataset for the investigation of gene regulatory networks in embryogenesis, and gained insight into the expression dynamics of the full complement of TFs controlling the development of each organ system.
authors.forename: Ann S
authors.initials: AS
authors.lastname: Hammonds
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Bristow
authors.forename: William W
authors.initials: WW
authors.lastname: Fisher
authors.forename: Richard
authors.initials: R
authors.lastname: Weiszmann
authors.forename: Siqi
authors.initials: S
authors.lastname: Wu
authors.forename: Volker
authors.initials: V
authors.lastname: Hartenstein
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: Bin
authors.initials: B
authors.lastname: Yu
authors.forename: Erwin
authors.initials: E
authors.lastname: Frise
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
mesh_terms: D000818:Animals; D002490:Central Nervous System / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics*; D004331:Drosophila melanogaster / Q000196:embryology* / Q000378:metabolism*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D017403:In Situ Hybridization; D009928:Organ Specificity; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D029721:Drosophila Proteins; D014157:Transcription Factors