Spatial expression of transcription factors in Drosophila embryonic organ development
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gb-2013-14-12-r140.pdf
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Author(s)
Hammonds, Ann S.
Fisher, William W.
Weiszmann, Richard
Wu, Siqi
Hartenstein, Volker
Kellis, Manolis
Yu, Bin
Frise, Erwin
Celniker, Susan E.
Bristow, Christopher A.
Date Issued
December 2013
Journal
Genome Biology
Publisher
BioMed Central Ltd
Citation
Hammonds, Ann S et al. “Spatial Expression of Transcription Factors in Drosophila Embryonic Organ Development.” Genome Biology 14.12 (2013): R140.
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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DOI of Published Version
https://doi.org/10.1186/gb-2013-14-12-r140
