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Series GSE32483 Query DataSets for GSE32483
Status Public on May 08, 2012
Title Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
Organism Danio rerio
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The generation of distinctive cell types that form different tissues and organs requires precise, temporal and spatial control of gene expression. This depends on specific cis-regulatory elements distributed in the non-coding DNA surrounding their target genes. Studies performed on mammalian embryonic stem cells and Drosophila embryos suggest that active enhancers form part of a defined chromatin landscape marked by histone H3 lysine 4 mono-methylation (H3K4me1) and histone H3 lysine 27 acetylation (H3K27ac). Nevertheless, little is known about the dynamics and the potential roles of these marks during vertebrate embryogenesis. Here we provide genomic maps of H3K4me1/me3 and H3K27ac at four developmental time-points of zebrafish embryogenesis and analyze embryonic enhancer activity. We find that: (i) changes in H3K27ac enrichment at enhancers accompany the shift from pluripotency to tissue-specific gene expression; (ii) in early embryos, the peaks of H3K27ac enrichment are bound by pluripotent factors such as Nanog; (iii) the degree of evolutionary conservation is higher for enhancers that become marked by H3K27ac at the end of gastrulation suggesting their implication in the establishment of the most conserved (phylotypic) transcriptome that is known to occur later at the pharyngula stage.
Overall design ChIP-seq analysis of H3K4me3, H3K4me1 and H3K27ac at four developmental time-points (dome, 80% epiboly, 24hpf and 48pf) of zebrafish embryogenesis.
Contributor(s) Bogdanović O, Fernandez-Miñan A, Tena JJ, de la Calle-Mustienes E, Hidalgo C, van Heeringen SJ, Veenstra GJ, Gómez-Skarmeta JL
Citation(s) 22593555
Submission date Sep 29, 2011
Last update date May 15, 2019
Contact name Ozren Bogdanovic
Organization name Garvan Institute of Medical Research
Department Genomics and Epigenetics
Street address 384 Victoria Street
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
Platforms (1)
GPL10164 Illumina Genome Analyzer (Danio rerio)
Samples (24)
GSM803822 H3K4me3_dome, danRer6
GSM803823 H3K4me3_80%epi, danRer6
GSM803824 H3K4me3_24hpf, danRer6
SRA SRP008826
BioProject PRJNA147789

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Supplementary file Size Download File type/resource
GSE32483_RAW.tar 2.0 Gb (http)(custom) TAR (of BED, WIG)
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Processed data provided as supplementary file
Raw data are available in SRA

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