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Series GSE58935 Query DataSets for GSE58935
Status Public on Oct 16, 2014
Title Establishment of regions of genomic activity during the Drosophila maternal-to-zygotic transition
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary A conspicuous feature of early animal development is the lack of transcription from the embryonic genome, and it typically takes several hours to several days (depending on the species) until widespread transcription of the embryonic genome begins. Although this transition is ubiquitous, relatively little is known about how the shift from a transcriptionally quiescent to transcriptionally active genome is controlled. We describe here the genome-wide distributions and temporal dynamics of nucleosomes and post-translational histone modifications through the maternal-to-zygotic transition in embryos of the pomace fly Drosophila melanogaster. At mitotic cycle 8, when few zygotic genes are being transcribed, embryonic chromatin is in a relatively simple state: there are few nucleosome-free regions, undetectable levels of the histone methylation marks characteristic of mature chromatin, and low levels of histone acetylation at a relatively small number of loci. Histone acetylation increases by cycle 12, but it is not until cycle 14 that nucleosome-free regions and domains of histone methylation become widespread. Early histone acetylation is strongly associated with regions that we have previously shown are bound in early embryos by the maternally deposited transcription factor Zelda. Most of these Zelda-bound regions are destined to be enhancers or promoters active during mitotic cycle 14, and our data demonstrate that they are biochemically distinct long before they become active, raising the possibility that Zelda triggers a cascade of events, including the accumulation of specific histone modifications, that plays a role in the subsequent activation of these sequences. Many of these Zelda-associated active regions occur in larger domains that we find strongly enriched for histone marks characteristic of Polycomb-mediated repression, suggesting a dynamic balance between Zelda activation and Polycomb repression. Collectively, these data paint a complex picture of a genome in transition from a quiescent to an active state, and highlight the role of Zelda in mediating this transition.
 
Overall design We performed genome-wide mapping of histone H3 and 9 types of histone modifications, including H4K5ac, H4K8ac, H3K4me1, H3K4me3, H3K27me3, H3K36me3, H3K9ac, H3K18ac, and H3K27ac by ChIP-seq, in hand-sorted wild-type Drosophila melanogaster embryos at 4 different development time points corresponding to mitotic cycle 7-9, 11-13, 14a-b, and 14c-d, respectively. We also carried out ChIP-seq experiments in zelda mutant embryos after showing that the deposition of histone marks in early embryos strongly correlated with the binding of Zelda in wild-type embryos.
 
Contributor(s) Li XY, Harrison MM, Kaplan T, Eisen MB
Citation(s) 25313869
Submission date Jun 30, 2014
Last update date Jan 23, 2019
Contact name Michael B Eisen
E-mail mbeisen@berkeley.edu
Organization name HHMI/Univ. California, Berkeley
Department MCB
Lab Mike Eisen
Street address 379 Stanley Hall, MC 3220
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (50)
GSM1424888 H4K5ac ChIP-seq at cycle 8
GSM1424889 H4K5ac ChIP-seq cycle 12
GSM1424890 H4K5ac ChIP-seq cycle 14a
Relations
BioProject PRJNA254188
SRA SRP044032

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
GSE58935_RAW.tar 1.1 Gb (http)(custom) TAR (of WIG, XLS)
Raw data are available in SRA
Processed data provided as supplementary file

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