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Series GSE137075 Query DataSets for GSE137075
Status Public on Feb 26, 2020
Title Developmentally regulated requirement for the conserved transcription factor Grainy head in determining chromatin accessibility
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design ATAC-seq chromatin accessibility profiling of Drosophila melanogaster embryos either wild-type or lacking maternal or zygotically expressed Grainy head at embryonic stages 5, 6, and 15
Please note that each narrowpeak data file was generated from all replicates and is linked to the corresponding rep1 sample records.
Contributor(s) Nevil M, Gibson TJ, Bartolutti C, Iyengar A, Harrison MM
Citation(s) 32098765
Submission date Sep 09, 2019
Last update date May 27, 2020
Contact name Melissa M Harrison
Organization name University of Wisconsin Madison
Department Biomolecular Chemistry
Lab 1135 Biochemical Sciences Bldg
Street address 420 Henry Mall
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
Platforms (3)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
GPL21306 Illumina HiSeq 4000 (Drosophila melanogaster)
GPL25244 Illumina NovaSeq 6000 (Drosophila melanogaster)
Samples (31)
GSM4066555 grhM-_stage5_rep1
GSM4066556 grhM-_stage5_rep2
GSM4066557 grhM-_stage5_rep3
BioProject PRJNA564514
SRA SRP221005

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE137075_RAW.tar 2.0 Gb (http)(custom) TAR (of BEDGRAPH, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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