Epigenetic regulation of key developmental genes in medaka Hiroyuki Takeda Department of Biological Sciences, Graduate School of Science, University of Tokyo In ES cells, “key developmental genes” are marked by specific modification called ‘bivalent’, co-existence of active (H3K4me) and repressive (H3K27me) histone modifications. The bivalent state becomes univalent (active or repressive) upon differentiation. Although extensive researches have been conducted using ES cells, in vivo evidence of this bivalency is still limited. Furthermore, the relationship between histone and DNA methylation has not been well studied thus far. To clarify these issues, we performed the genome-wide DNA methylome analysis as well as ChIP-seq analysis of H3K4me and H3K27me using the undifferentiated blastula-stage embryos of medaka fish. We found that most of the genomic DNA is highly methylated but loci where H3K4 and/or H3K27 methylation occur are hypomethylated. Among them, ~200 loci possess long DNA hypomethylated domain (>5kb) with bivalent histone modifications. Interestingly, ~75 % of genes within such loci were found to be key developmental genes including transcriptional regulators such as homeobox and T-box genes. The same analysis using adult liver and muscle revealed that DNA methylation is up-regulated, except for H3K4me-rich promoter regions, in actively transcribed loci. The further analysis focused on the zic gene, one of these loci, demonstrated that DNA methylation proceeds after hatching, whereas histone modification is established during embryonic stages. We propose that key developmental genes are regulated in a step-wise manner throughout life, bivalent and DNA hypomethylated state in undifferentiated early embryos, histone-modification-dependent induction during development and finally the maintenance of transcription by DNA-methylation after birth.

Epigenetic regulation of key developmental genes in medaka

Hiroyuki Takeda

Department of Biological Sciences, Graduate School of Science, University of Tokyo

In ES cells, “key developmental genes” are marked by specific modification called ‘bivalent’, co-existence of active (H3K4me) and repressive (H3K27me) histone modifications. The bivalent state becomes univalent (active or repressive) upon differentiation. Although extensive researches have been conducted using ES cells, in vivo evidence of this bivalency is still limited. Furthermore, the relationship between histone and DNA methylation has not been well studied thus far. To clarify these issues, we performed the genome-wide DNA methylome analysis as well as ChIP-seq analysis of H3K4me and H3K27me using the undifferentiated blastula-stage embryos of medaka fish. We found that most of the genomic DNA is highly methylated but loci where H3K4 and/or H3K27 methylation occur are hypomethylated. Among them, ~200 loci possess long DNA hypomethylated domain (>5kb) with bivalent histone modifications. Interestingly, ~75 % of genes within such loci were found to be key developmental genes including transcriptional regulators such as homeobox and T-box genes. The same analysis using adult liver and muscle revealed that DNA methylation is up-regulated, except for H3K4me-rich promoter regions, in actively transcribed loci. The further analysis focused on the zic gene, one of these loci, demonstrated that DNA methylation proceeds after hatching, whereas histone modification is established during embryonic stages. We propose that key developmental genes are regulated in a step-wise manner throughout life, bivalent and DNA hypomethylated state in undifferentiated early embryos, histone-modification-dependent induction during development and finally the maintenance of transcription by DNA-methylation after birth.