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

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 developmentallyregulated 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 developmentallyregulated 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 for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm

“…Loci of developmental importance in the embryo bear complex multivalent chromatin in sperm and resemble several ways the chromatin present at these loci during MBT, when developmental loci must be repressed but able to be activated (Hammoud et al 2009;Lindeman et al 2010;Vastenhouw et al 2010). Indeed, work from several laboratories now suggests that totipotent/pluripotent states of the germline and embryos share at developmental promoters unmethylated and complex ''multivalent'' chromatin (Hammoud et al 2009;Lindeman et al 2010;Vastenhouw et al 2010).…”

“…Indeed, work from several laboratories now suggests that totipotent/pluripotent states of the germline and embryos share at developmental promoters unmethylated and complex ''multivalent'' chromatin (Hammoud et al 2009;Lindeman et al 2010;Vastenhouw et al 2010). A clear question is whether this complex multivalent chromatin built in the sperm is needed solely for the proper gene regulation in the germline, or whether this multivalent chromatin (or any portion) is maintained and instructive in the embryo.…”

Chromatin states in pluripotent, differentiated, and reprogrammed cells

“…Bivalent chromatin is found within the ICM and trophectoderm in mice and in zebrafish pre-gastrulation embryos [37][38][39]40 ]. Bivalent chromatin is also present, albeit less frequently than in ESCs, in neural progenitors, mesenchymal stem cells, and hematopoietic stem and progenitor cells, and tends to resolve upon further differentiation [41,[42][43][44][45].…”

Developmentally arrested Austrofundulus limnaeus embryos have changes in post-translational modifications of histone H3

“…Histone H3 post-translational modifications are extensively studied because of their impact on chromatin structure and function and their central role in epigenetic mechanisms. However, our understanding of chromatin modification in developing vertebrate embryos is limited and has only been examined in a few species including mice (Dahl et al, 2010;VerMilyea et al, 2009), zebrafish (Havis et al, 2006;Lindeman et al, 2010;Wardle et al, 2006), N. furzeri (Baumgart et al, 2014) and Xenopus tropicalis embryos (van Heeringen et al, 2014). The chromatin state in an arrested vertebrate embryo has not been fully examined.…”

“…How the chromatin landscape influences gene expression has been extensively studied in yeast and mammalian cells grown in culture but less is understood about chromatin modifications relative to the developmental stages of vertebrate embryos (Bannister and Kouzarides, 2011;Kishi, 2014;Martinez-Sales et al, 2014). The post-translational modifications of histones have been mapped in mice embryos (Dahl et al, 2010;VerMilyea et al, 2009), zebrafish Danio rerio (Havis et al, 2006;Lindeman et al, 2010;Wardle et al, 2006) and Xenopus tropicalis embryos (van Heeringen et al, 2014). Together, these studies indicate that histone modifications are associated with developmentally regulated genes.…”