Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enhancers reside in a unique epigenetic environment during early development

ABSTRACT: During development and differentiation, enhancers, and not promoters are most dynamic in their DNA methylation status. However, the causal relationship between enhancer activity and methylation is not clear. Here, we describe that during early zebrafish development, enhancer activity has little influence on DNA methylation, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the maternal-zygotic transition (MZT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity. In conclusion, we demonstrate that early development in zebrafish represents a time-window characterized by non-canonical DNA methylation-enhancer relationships, including global DNA hypo-methylation of inactive enhancers and DNA hyper-methylation of active enhancers.

ORGANISM(S): Danio rerio

PROVIDER: GSE74789 | GEO | 2015/11/09

SECONDARY ACCESSION(S): PRJNA301526

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Enhancers reside in a unique epigenetic environment during early development

Project description:During development and differentiation, enhancers, and not promoters are most dynamic in their DNA methylation status. However, the causal relationship between enhancer activity and methylation is not clear. Here, we describe that during early zebrafish development, enhancer activity has little influence on DNA methylation, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the maternal-zygotic transition (MZT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity. In conclusion, we demonstrate that early development in zebrafish represents a time-window characterized by non-canonical DNA methylation-enhancer relationships, including global DNA hypo-methylation of inactive enhancers and DNA hyper-methylation of active enhancers. DNA methylation profiles of 4 time points during zebrafish early development.

2015-11-09 | E-GEOD-74789 | biostudies-arrayexpress

Enhancers reside in a unique epigenetic environment during early zebrafish development [4C-seq]

Project description:We describe that during early zebrafish development, DNA methylation has little influence on enhancer activity, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are generally hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the mid blastula transition (MBT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active later in development and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity. We performed 6 different 4C-Seq experiment at two different timepoints and in adult brain.

2015-11-06 | E-GEOD-74616 | biostudies-arrayexpress

Enhancers reside in a unique epigenetic environment during early zebrafish development [ChIP-seq & ATAC-seq]

Project description:We describe that during early zebrafish development, DNA methylation has little influence on enhancer activity, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are generally hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the mid blastula transition (MBT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active later in development and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity. we analyzed 5 novel ChIP-Seq libraries where we used the following AB (H3K27ac,H3K4me1,H3K4me2 and H3K27ac) and an Atac-Seq library.

2015-11-06 | E-GEOD-74231 | biostudies-arrayexpress

Enhancers reside in a unique epigenetic environment during early zebrafish development [4C-seq]

2015-11-06 | GSE74616 | GEO

Enhancers reside in a unique epigenetic environment during early zebrafish development [ChIP-seq & ATAC-seq]

2015-11-06 | GSE74231 | GEO

Active DNA demethylation during the vertebrate phylotypic period

Project description:The vertebrate body plan and organs are shaped during a highly conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report widespread DNA demethylation of thousands of enhancers during the phylotypic period in zebrafish, Xenopus and mouse. These dynamic enhancers are linked to essential developmental genes that display coordinated transcriptional and epigenomic changes in the diverse vertebrates during embryogenesis. Phylotypic stage-specific binding of Tet proteins to (hydroxy)methylated DNA, and enrichment of hydroxymethylcytosine on these enhancers, implicated active DNA demethylation in this process. Furthermore, loss of function of Tet1/2/3 in zebrafish caused reduced chromatin accessibility and increased methylation levels specifically on these enhancers, indicative of DNA methylation being an upstream regulator of phylotypic enhancer function. Overall, our study reveals a novel regulatory module associated with the most conserved phase of vertebrate embryogenesis and uncovers an ancient developmental role for the Tet dioxygenases.

2016-01-27 | PXD001164 | Pride

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MRE-seq)

Project description:DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis. MRE profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.

2015-02-13 | E-GEOD-52704 | biostudies-arrayexpress

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MeDIP-seq)

Project description:DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis. MeDIP profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.

2015-02-13 | E-GEOD-52703 | biostudies-arrayexpress

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MRE-seq)

2015-02-13 | GSE52704 | GEO

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MeDIP-seq)

2015-02-13 | GSE52703 | GEO