Genomics

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321

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis


ABSTRACT: 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. ChIP-seq analysis of H3K4me3, H3K4me1 and H3K27ac at four developmental time-points (dome, 80% epiboly, 24hpf and 48pf) of zebrafish embryogenesis.

ORGANISM(S): Danio rerio  

SUBMITTER: José L Gómez-Skarmeta   Juan J Tena  Gert J Veenstra  Carmen Hidalgo  Ozren Bogdanovic  Ana Fernandez-Miñan  Elisa de la Calle-Mustienes  Ozren Bogdanović  Simon J van Heeringen 

PROVIDER: E-GEOD-32483 | ArrayExpress | 2012-05-08

SECONDARY ACCESSION(S): GSE32483SRP008826PRJNA147789

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.

Bogdanovic Ozren O   Fernandez-Miñán Ana A   Tena Juan J JJ   de la Calle-Mustienes Elisa E   Hidalgo Carmen C   van Kruysbergen Ila I   van Heeringen Simon J SJ   Veenstra Gert Jan C GJ   Gómez-Skarmeta José Luis JL  

Genome Research 20120516 10


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 noncoding 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 acetylati  ...[more]

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