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

Abstract

It has been suggested that transcription factor binding is temporally dynamic, and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head (Grh) is conserved from fungi to humans, and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head (grh) gene, provide an excellent system to study this conserved factor. To determine whether temporally distinct binding events allow Grh to control cell fate specification in different tissue types, we used a combination of ChIP-seq and RNA-seq to elucidate the gene regulatory network controlled by Grh during four stages of embryonic development (spanning stages 5-17) and in larval tissue. Contrary to expectations, we discovered that Grh remains bound to at least 1146 genomic loci over days of development. In contrast to this stable DNA occupancy, the subset of genes whose expression is regulated by Grh varies. Grh transitions from functioning primarily as a transcriptional repressor early in development to functioning predominantly as an activator later. Our data reveal that Grh binds to target genes well before the Grh-dependent transcriptional program commences, suggesting it sets the stage for subsequent recruitment of additional factors that execute stage-specific Grh functions.

Novel role for Grainy head in the regulation of cytoskeletal and junctional dynamics during epithelial repair

“…Here, we show that dl expression is increased in grh mutant embryos, suggesting that Grh might repress dl. This is supported by other studies showing that the transcription starting site of dl contains a presumptive binding domain for Grh (Potier et al, 2014), and that the expression of Drosomycin, a bona fide target of Dl, is increased in grh mutant embryos in comparison to wild type (Nevil et al, 2017;Paré et al, 2012). The regulation of Dl by Grh might be especially relevant during wound healing.…”

Enhancer architecture sensitizes cell specific responses toNotchgene dose via a bind and discard mechanism

“…Since Grh binding is sufficient to increase chromatin opening (Jacobs, et al, 2018), these findings suggest enhancer accessibility alters the rate at which NICD is metabolized by Notch dimer sites. Intriguingly, published ChIP data (Nevil, et al, 2017) reveals Grh binds extensively to the Enhancer of Split (E(spl)) locus that has numerous SPScontaining Notch regulated enhancers (Cave, et al, 2011;Cooper, et al, 2000;Nellesen, et al, 1999). Thus, these data highlight a potential mechanism by which enhancer architecture (i.e.…”

Extraction of Hemocytes from <em>Drosophila melanogaster</em> Larvae for Microbial Infection and Analysis

“…For example, Kurucz et al, have developed antibodies that could be used to isolate the Drosophila hemocyte subsets that could be used for transcriptional or proteomic profiling following various stimuli. Additionally, the recent development of single cell RNAseq technology could define transcriptomes of each cell type without the use of antibodies to initially separate each cell type36,37,38,39. Furthermore, one could ask questions regarding gene regulation in the hemocyte subsets that may help us understand how human blood cell lineages originated and evolved from ancient organisms through comparative genomics efforts.…”