Spatial expression of transcription factors in Drosophilaembryonic organ development

Abstract

BackgroundSite-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.ResultsWe 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.ConclusionsWe 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.

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes ThroughoutDrosophila melanogasterDevelopment

“…For one of these genes, hgo, we further confirmed this Grh-mediated expression in vivo by assaying expression of a lacZ transgene driven by either the wild-type hgo promoter or one harboring mutations in the identified Grh-binding site ( Figure 5C). The expression pattern of lacZ driven by the wild-type hgo promoter resembles expression of the endogenous gene as reported by the Berkeley Drosophila Genome Project (Tomancak et al 2002(Tomancak et al , 2007Hammonds et al 2013). Mutations in the single canonical Grh-binding motif result in background levels of staining ( Figure 5C).…”

A framework for understanding the roles of miRNAs in animal development

“…One potential explanation for this could be that more miRNAs than TFs are expressed in highly restricted manner. Indeed, although it looks like a large fraction of miRNAs could fall into this 'highly restricted' category, a systematic study in Drosophila embryos shows that out of ∼700 TFs only 20% show 'single-organ specificity', and the majority are expressed across multiple organ systems (Hammonds et al, 2013). However, more systematic expression analyses allowing comparisons within species are needed to address this issue further.…”

Drosophilapoised enhancers are generated during tissue patterning with the help of repression

“…A target gene was assigned to DV enhancers only if the enhancer's expression domain overlapped and resembled the gene's expression domain (Supplemental Material). For this purpose, published mRNA in situ hybridization data from the Berkeley Drosophila Genome Project (BDGP) (Tomancak et al 2002(Tomancak et al , 2007Hammonds et al 2013) database were used for enhancers identified by Kvon et al (2012) and Ozdemir et al (2011). For some of these enhancers, no target gene was identified with confidence, and thus those enhancers were not included in mRNA-seq analysis shown in Supplemental Figure S1 (Supplemental Material).…”