Expression profiling by high throughput sequencing
Summary
Transcription factors (TFs) play a key role in development and in cellular responses to the environment by activating or repressing the transcription of target genes in precise spatial and temporal patterns. In order to develop a catalog of target genes of D. melanogaster transcription factors, the modERN consortium systematically knocked down expression of transcription factors (TFs) using RNAi in whole embryos followed by RNA-seq. We generated data for 45 TFs which have 18 different DNA-binding domains and are expressed in 15 of the 16 organ systems. The range of inactivation of the targeted TFs by RNAi ranged from log2fold change -3.52 to +0.49. The TFs also showed remarkable heterogeneity in the numbers of candidate target genes identified, with some generating thousands of candidates and others only tens. We present detailed analysis from six experiments, including those for four TFs that have been the focus of previous functional studies (ERR, sens, su(Hw) and zfh2) and two previously uncharacterized TFs (sens-2 and CG32006), as well as short vignettes from selected additional experiments to illustrate the utility of this resource. Transcription Factor and target gene expression patterns can be found here: https://insitu.fruitfly.org. These studies provide data that facilitate scientific inquiries into the functions of individual TFs in key developmental, metabolic, defensive, and homeostatic regulatory pathways, as well as provide a broader perspective on how individual TFs work together in local networks during embryogenesis.
Overall design
Transcription factors were knocked down using RNAi, and the effect of gene expression was evaluated by paired-end RNA-seq in replicate.
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