PUBLICATION
Reprogramming histone modification patterns to coordinate gene expression in early zebrafish embryos
- Authors
- Zhu, W., Xu, X., Wang, X., Liu, J.
- ID
- ZDB-PUB-190330-1
- Date
- 2019
- Source
- BMC Genomics 20: 248 (Journal)
- Registered Authors
- Keywords
- Conservation, Early embryo, Epigenetics, Histone modification, Reprogramming
- Datasets
- GEO:GSE110663
- MeSH Terms
-
- Animals
- DNA Methylation*
- Embryo, Nonmammalian/metabolism
- Epigenesis, Genetic
- Female
- Gene Expression Profiling/methods*
- Gene Expression Regulation, Developmental
- Histone Code
- Histones/metabolism*
- Male
- Oocytes/chemistry
- Promoter Regions, Genetic
- Protein Processing, Post-Translational
- Spermatozoa/chemistry
- Zebrafish/embryology*
- Zebrafish/genetics
- Zebrafish/metabolism
- Zebrafish Proteins/genetics*
- Zebrafish Proteins/metabolism
- PubMed
- 30922236 Full text @ BMC Genomics
Citation
Zhu, W., Xu, X., Wang, X., Liu, J. (2019) Reprogramming histone modification patterns to coordinate gene expression in early zebrafish embryos. BMC Genomics. 20:248.
Abstract
Background Multicellular organisms require precise gene regulation during ontogeny, and epigenetic modifications, such as DNA methylation and histone modification, facilitate this precise regulation. The conservative reprogramming patterns of DNA methylation in vertebrates have been well described. However, knowledge of how histone modifications are passed on from gametes to early embryos is limited, and whether histone modification reprogramming is conserved is not clear.
Results We profiled H3K4me3/H3K27me3 modifications in gametes and early embryos in zebrafish and found that the patterns in gene promoter regions have been largely set to either co-occupied or active states in gametes and then passed on to early embryos. Co-occupied states are partially maintained, while active states are largely restored to nearly match the sperm's pattern prior to zygotic genome activation (ZGA). However, repressive H3K27me3 modifications in promoter regions are largely discarded in early embryos. Prior to ZGA, patterns of genes that initialize ZGA are converted to nonrepressive states to coordinate gene expression. Moreover, promoter peaks that mark stage-specific genes are hypermethylated, and histone modifications in these regions are erased independently of DNA methylation reprogramming. Furthermore, comparative analysis revealed that the functions of co-occupied and active genes passed on from gametes are conserved in vertebrates. Gene age preferences by co-occupied and active histone modifications are also confirmed in vertebrates.
Conclusions Our data provide fundamental resources for understanding H3K4me3/H3K27me3 modifications in early zebrafish embryos. The data also reveal that the reprogramming progress of histone modifications is conserved in vertebrates and coordinates with gene expression during ZGA.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping