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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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.

ORGANISM(S): Danio rerio

SUBMITTER: lucas kaaij

PROVIDER: E-GEOD-74616 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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

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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 development

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Project description:Zygotic genome activation (ZGA) occurs at the mid-blastula transition (MBT) in zebrafish and is a period of chromatin remodeling. Genome-scale gametic demethylation and remethylation occurs after fertilization, during blastula stages, but how ZGA relates to promoter DNA methylation states is unknown. Using methylated DNA immunoprecipitation coupled to high-density microarray hybridization (MeDIP-ChIP), we characterize genome-wide promoter DNA methylation dynamics before, during and after ZGA onset, in relation changes in post-translational histone modification and gene expression (Series GSE22830). A Kolmogorov-Smirnov (KS) test was applied with P <= 0.01 to identify methylation peaks.

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Study of Mid-Blastula Transition of zebrafish embryos

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Marking of the genome by H3K4 methylation prior to embryonic gene activation

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