PUBLICATION

Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos

Authors
Lindeman, L.C., Winata, C.L., Aanes, H., Mathavan, S., Alestrom, P., and Collas, P.
ID
ZDB-PUB-100330-25
Date
2010
Source
The International journal of developmental biology   54(5): 803-813 (Journal)
Registered Authors
Collas, Philippe, Mathavan, S., Winata, Cecilia Lanny
Keywords
Danio rerio, DNA methylation, embryo, gene expression, histone modification, zebrafish
Datasets
GEO:GSE20137
MeSH Terms
  • Animals
  • Blastula/embryology
  • Blastula/metabolism
  • Cell Line
  • Chromatin/genetics
  • Chromatin/metabolism*
  • Chromatin Immunoprecipitation
  • CpG Islands/genetics
  • DNA Methylation*
  • Embryo, Nonmammalian/embryology
  • Embryo, Nonmammalian/metabolism*
  • Fibroblasts/cytology
  • Fibroblasts/metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Histones/metabolism*
  • In Situ Hybridization
  • Lysine/metabolism
  • Methylation
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic/genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Zebrafish/embryology
  • Zebrafish/genetics*
  • Zebrafish/metabolism
  • Zebrafish Proteins/genetics*
  • Zebrafish Proteins/metabolism
PubMed
20336603 Full text @ Int. J. Dev. Biol.
Abstract
Embryo development proceeds from a cascade of gene activation and repression events controlled by epigenetic modifications of DNA and histones. Little is known about epigenetic states in the developing zebrafish, despite its importance as a model organism. We report here DNA methylation and histone modification profiles of promoters of developmentally-regulated genes (pou5f1, sox2, sox3, klf4, nnr, otx1b, nes, vasa), as well as tert and bactin2, in zebrafish embryos at the mid-late blastula transition, shortly after embryonic genome activation. We identify four classes of promoters based on the following profiles: (i) those enriched in marks of active genes (H3K9ac, H4ac, H3K4me3) without transcriptionally repressing H3K9me3 or H3K27me3; (ii) those enriched in H3K9ac, H4ac and H3K27me3, without H3K9me3; one such gene was klf4, shown by in situ hybridization to be mosaically expressed, likely accounting for the detection of both activating and repressive marks on its promoter; (iii) those enriched in H3K4me3 and H3K27me3 without acetylation; and (iv) those enriched in all histone modifications examined. Culture of embryo-derived cells under differentiation conditions leads to H3K9 and H4 deacetylation and H3K9 and H3K27 trimethylation on genes that are inactivated, yielding an epigenetic profile similar to those of fibroblasts or muscle. All promoters however retain H3K4me3, indicating an uncoupling of H3K4me3 occupancy and gene expression. All non-CpG island developmentally-regulated promoters are DNA unmethylated in embryos, but hypermethylated in fibroblasts. Our results suggest that differentially expressed embryonic genes are regulated by various patterns of histone modifications on unmethylated DNA, which create a developmentally permissive chromatin state.
Genes / Markers
Figures
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Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping