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SRX645118: GSM1424907: H3K4me1 ChIP-seq cycle 14c; Drosophila melanogaster; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 42.4M spots, 4.2G bases, 2.7Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Establishment of regions of genomic activity during the Drosophila maternal-to-zygotic transition
show Abstracthide Abstract
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.
Sample: H3K4me1 ChIP-seq cycle 14c
SAMN02900693 • SRS653300 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: 7.5, 0.7, 0.4, and 0.3 g of embryos at four different stages, respectively, were used to prepare chromatin for immunoprecipitation following the CsCl2 gradient ultracentrifugation protocol as previously described (Harrison et al., 2011).The chromatin obtained was fragmented to sizes ranging from 100 to 300 bp using a Bioruptor (Diagenode, Inc.) for a total processing time of 140 min (15 s on, 45 s off), with power setting at "H". Prior to carrying out chromatin immunoprecipitation, we mixed the chromatin from each sample with a roughly equivalent amount of chromatin isolated from stage 5 (mitotic cycle 14) D. pseudoobscura embryos, and used about 2 µg of total chromatin (1 µg each of the D. melanogaster and D. pseudoobscura chromatin) for each chromatin immunoprecipitation. The chromatin immunoprecipitation reactions were carried out as described previously (Harrison et al., 2011) with 0.5 ug anti-H4K5ac (Millipore, 07-327), 0.5 ug anti-H3K4me3 (Abcam, ab8580), 0.5 ug anti-H3K27ac (Abcam, ab4729), 1 ug anti-H3 (Abcam, ab1791), 0.75 ug anti-H3K4me1 (Abcam, ab8895), 0.75 ug anti-H4K8ac (Abcam, ab15823), 1.5 ul anti-H3K9ac (Activemotif, 39138), 0.75 ug anti-H3K18ac (Abcam, ab1191), 3 ug anti-H3K27me3 (Millipore, 07-449), or 0.75 ug anti-H3K36me3 (Abcam, ab9050). The sequencing libraries were prepared from the ChIP and Input DNA samples using the Illumina TruSeq DNA Sample Preparation kit following the manufacturer's instructions, and DNA was subjected to ultra-high-throughput sequencing on Illumina HiSeq 2000 DNA sequencers. The libraries were combined into pools, with each containing 6-8 libraries with different index and at similar concentrations, and each library pool was sequenced (100 bp single-end read) in a single lane in a flow cell.
Experiment attributes:
GEO Accession: GSM1424907
Links:
External link:
Runs: 1 run, 42.4M spots, 4.2G bases, 2.7Gb
Run# of Spots# of BasesSizePublished
SRR150571842,356,4264.2G2.7Gb2014-10-16

ID:
901568

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