Project description: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.
Project description:Pioneer transcription factors initiate changes in gene expression by binding to cis-regulatory modules and promoting chromatin accessibility. It is suggested that this activity is an essential first step in priming these sites for the binding of other factors. Nonetheless, it is unclear whether pioneering activity is always required when these factors are present during development. The highly conserved, essential transcription factor Grainy head was recently identified as a pioneer factor in Drosophila larval imaginal discs, yet Grainy head is present throughout development. To determine whether Grainy head maintains its pioneering role throughout development, we performed ATAC-seq on embryos lacking either maternal or zygotic Grainy head at three stages of development (stage 5, stage 6, and stage 15). Surprisingly, we discovered that neither maternal nor zygotic Grainy head are required for chromatin accessibility in early embryogenesis. Nonetheless, we find that Grainy head binding is correlated with some cis-regulatory modules that gain chromatin accessibility at gastrulation. Intriguingly, later in embryogenesis Grainy head gains a role in promoting chromatin accessibility. Additionally, we determined that Grainy head is able to remain bound to mitotic chromatin, like other pioneer factors, yet this ability is separate from its pioneering activity. Our data reveal that Grainy head pioneering activity is temporally, suggesting that other unidentified pioneer factors compensate for the loss of Grainy head.
Project description:To determine the genes directly and indirectly under the control of the Grainy head transcription factor during late stages of Drosophila embryogenesis.
Project description:To determine the genes directly and indirectly under the control of the Grainy head transcription factor during late stages of Drosophila embryogenesis. Total RNA from pre-larval (late stage 16 and early stage 17) grhIM homozygous (+; cn, grhIM, bw, sp; +) and wild-type (y; cn, bw, sp; +) embryos were compared.
Project description:To determine the genes directly and indirectly under the control of the Grainy-head homolog (GHH) transcription factor in Neurospora crassa Three different sample types (Aerial Hyphae & Conidia; Mycelia; or Whole Colonies) of both wild-type (FGSC #2489) and grainy-head homolog (FGSC #13563) strains of Neurospora crassa were subjected to transcriptome analyses to determine the genes differentially expressed in the ghh background compared to wild type.
Project description:Raw Data Files for investigation into the usage of micro push-pull perfusion probes to sample drosophila melanogaster brain in vivo, as well as sampling hemolymph from head and abdomen anatomical regions.
Project description:To verify unannotated translated open reading frames (utORFs) identified from Drosophila melanogaster, we collected data to target them.
