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Developmentally regulated requirement for the conserved transcription factor Grainy head in determining chromatin accessibility

ABSTRACT: Developmentally regulated requirement for the conserved transcription factor Grainy head in determining chromatin accessibility

PROVIDER: PRJNA564514 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10084519_1.fastq.gz	Fastqsanger.gz
	SRR10084519_2.fastq.gz	Fastqsanger.gz
	SRR10084520_1.fastq.gz	Fastqsanger.gz
	SRR10084520_2.fastq.gz	Fastqsanger.gz
	SRR10084521_1.fastq.gz	Fastqsanger.gz

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Developmentally regulated requirement for the conserved transcription factor Grainy head in determining chromatin accessibility

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.

2020-02-26 | GSE137075 | GEO

Characterization of late-stage Drosophila grainy head IM-allele (grhIM) mutant embryos

Project description:To determine the genes directly and indirectly under the control of the Grainy head transcription factor during late stages of Drosophila embryogenesis.

2012-03-01 | GSE34997 | GEO

Characterization of late-stage Drosophila grainy head IM-allele (grhIM) mutant embryos

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.

2012-03-01 | E-GEOD-34997 | biostudies-arrayexpress

Stable Binding of the Conserved Transcription Factor Grainy Head to Its Target Genes Throughout Drosophila melanogaster Development

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.

2017-02-02 | GSE83305 | GEO

Genome-wide identification of Grainy head targets in Drosophila

Project description:Genome-wide identification of Grainy head targets in Drosophila

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Characterization of Neurospora crassa ghh (NCU06095) mutant strains

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.

2012-03-01 | E-GEOD-35017 | biostudies-arrayexpress

Characterization of Neurospora crassa ghh (NCU06095) mutant strains

Project description:To determine the genes directly and indirectly under the control of the Grainy-head homolog (GHH) transcription factor in Neurospora crassa

2012-03-01 | GSE35017 | GEO

Establishment of chromatin accessibility by the conserved transcription factor Grainy head is developmentally regulated.

Project description:The dramatic changes in gene expression required for development necessitate the establishment of cis-regulatory modules defined by regions of accessible chromatin. Pioneer transcription factors have the unique property of binding closed chromatin and facilitating the establishment of these accessible regions. Nonetheless, much of how pioneer transcription factors coordinate changes in chromatin accessibility during development remains unknown. To determine whether pioneer-factor function is intrinsic to the protein or whether pioneering activity is developmentally modulated, we studied the highly conserved, essential transcription factor Grainy head (Grh). Prior work established that Grh is expressed throughout Drosophila development and is a pioneer factor in the larva. We demonstrated that Grh remains bound to mitotic chromosomes, a property shared with other pioneer factors. By assaying chromatin accessibility in embryos lacking maternal and/or zygotic Grh at three stages of development, we discovered that Grh is not required for chromatin accessibility in early embryogenesis, in contrast to its essential functions later in development. Our data reveal that the pioneering activity of Grh is temporally regulated and likely influenced by additional factors expressed at a given developmental stage.

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An evolutionary conserved Sp5-Wnt3 regulatory module contributes to restrict head organizer activity in Hydra

Project description:Head regeneration in Hydra requires the transformation of gastric tissue into a head organizer that produces a head activator and a head inhibitor. Here we report the decipherment of a long-standing question in developmental biology, the identification of the transcription factor Sp5 as a key head inhibitory component. We show that Sp5 has an apical to basal graded expression pattern in intact Hydra, its expression is induced upon Wnt/β-catenin signaling activation and when knocked-down triggers the formation of multiple heads and axes in homeostatic and regenerative conditions. Our data indicate that Sp5 acts in a feed-forward loop to robustly regulate its own expression and that Sp5 prevents head formation by repressing the Wnt3 promoter. This Sp5 mediated Wnt antagonism is conserved and was invented early in metazoan evolution to set up axial patterning.

2019-03-01 | GSE110277 | GEO