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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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Enhancer chromatin signatures predict Smad2/3 binding in Xenopus

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

2014-09-17 | E-GEOD-56000 | biostudies-arrayexpress

Xenopus tropicalis x Xenopus laevis

Project description:Single-base resolution methylomes of Xenopus laevis x Xenopus tropicalis embryos

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Xenopus tropicalis

Project description:Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

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Transcription profiling of Xenopus tropicalis oocytes during maturation and early cleavage stages to identify post-transcriptionally regulated Xenopus tropicalis maternal mRNAs

Project description:Determine the adenylation state of maternal mRNAs during oocyte maturation and early cleavage stages of the xenopus tropicalis embryos

2007-09-30 | E-MEXP-1236 | biostudies-arrayexpress

Transcriptomics of Dorso-Ventral axis determination in Xenopus tropicalis

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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Project description:Epigenomic profiling (H3K4me1, H3K4me3, H3K36me3, p300 and RNA Polymerase II) of Xenopus laevis stage 10.5 embryos.

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Whole embryo depletion of Taf15 in gastrula and neurula stage Xenopus tropicalis embryos

Project description:We examined the role of Taf15 in in gastrula and neurula stage Xenopus tropicalis embryos.

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Project description:To correlate 5fC clusters with RNA polymerase III occupancy genome-wide, we carried out Pol III ChIP-seq profiling in Xenopus tropicalis blastula embryos.

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