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Xenopus tropicalis

ABSTRACT: A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

PROVIDER: PRJNA112449 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR029238.fastq.gz	Fastqsanger.gz
	SRR029239.fastq.gz	Fastqsanger.gz
	SRR029240.fastq.gz	Fastqsanger.gz
	SRR029241.fastq.gz	Fastqsanger.gz
	SRR029242.fastq.gz	Fastqsanger.gz

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A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

Project description:Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryogenesis. Here, we report on the epigenetic and transcriptome genome-wide maps of gastrula-stage Xenopus tropicalis embryos using massive parallel sequencing of cDNA (RNA-seq) and DNA obtained by chromatin immunoprecipitation (ChIP-seq) of histone H3 K4 and K27 trimethylation and RNA Polymerase II (RNAPII). These maps identify promoters and transcribed regions. Strikingly, genomic regions featuring opposing histone modifications are mostly transcribed, reflecting spatially regulated expression rather than bivalency as determined by expression profile analyses, sequential ChIP, and ChIP-seq on dissected embryos. Spatial differences in H3K27me3 deposition are predictive of localized gene expression. Moreover, the appearance of H3K4me3 coincides with zygotic gene activation, whereas H3K27me3 is predominantly deposited upon subsequent spatial restriction or repression of transcriptional regulators. These results reveal a hierarchy in the spatial control of zygotic gene activation. ChIP-seq profiles of two histone modifications (H3K4me3 and H3K27me3) and RNA Polymerase II, and a RNA-seq profile, of gastrula stage Xenopus tropicalis embryos

2009-09-15 | E-GEOD-14025 | biostudies-arrayexpress

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

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Project description:In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic transcription and continuing through gastrulation. We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq

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Project description:We studied the transcriptomic differences between ventralised and dorsalised Xenopus tropicalisembryos as a result of UV irradiation and LiCl treatment, respectvely. Both manipulations have been used by researchers to perturb the establishment of the dorso-ventral axis, however the whole transcriptomes of the resulting embryos have never been fully characterised or compared. We show that ventralized embryos are transcriptionally closer related to untreated embryos than dorsalized embryos. Furthermore comparison to dissected ventral and dorsal parts of an unperturbed gastrula embryo indicates that UV and LiCl treatment indeed enriches for ventral and dorsal cells, respectively.

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