PUBLICATION

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

Authors
Lee, H.J., Lowdon, R.F., Maricque, B., Zhang, B., Stevens, M., Li, D., Johnson, S.L., Wang, T.
ID
ZDB-PUB-150224-20
Date
2015
Source
Nature communications   6: 6315 (Journal)
Registered Authors
Johnson, Stephen L., Lee, Hyung Joo, Zhang, Bo
Keywords
none
Datasets
GEO:GSE52704, GEO:GSE52706, GEO:GSE52703
MeSH Terms
  • Gene Library
  • Epigenesis, Genetic
  • Promoter Regions, Genetic
  • Histones/chemistry
  • Female
  • Embryonic Development/genetics
  • Gene Expression Regulation, Developmental*
  • Green Fluorescent Proteins/metabolism
  • CpG Islands
  • DNA Methylation*
  • Animals
  • Enhancer Elements, Genetic*
  • Signal Transduction
  • Male
  • Gene Regulatory Networks
  • DNA/metabolism
  • Zebrafish/embryology*
  • Sequence Analysis, DNA
(all 18)
PubMed
25697895 Full text @ Nat. Commun.
Abstract
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.
Genes / Markers
Figures
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Expression
Phenotype
No data available
Mutations / Transgenics
No data available
Human Disease / Model
No data available
Sequence Targeting Reagents
No data available
Fish
No data available
Antibodies
No data available
Orthology
No data available
Engineered Foreign Genes
No data available
Mapping
No data available