| Description |
One central question in development is how totipotency and pluripotency are established. In mature human sperm, genes of importance for embryo development (i.e. transcription factors) lack DNA methylation and bear nucleosomes with distinctive histone modifications, suggesting the specialized packaging of these developmental genes in the germline. Here, we explored the tractable zebrafish model and found conceptual conservation as well as several new features. Biochemical and mass spectrometric approaches reveal the zebrafish sperm genome packaged in nucleosomes and histone variants (and not protamine), and we find linker histones high and H4K16ac absent-key factors which may contribute to genome condensation. We examined several activating (H3K4me2/3, H3K14ac, H2AFV) and repressing (H3K27me3, H3K36me3, H3K9me3, hypoacetylation) modifications/compositions genome-wide, and find developmental genes packaged in large blocks of chromatin with coincident activating and repressing marks and DNA hypomethylation, revealing complex "multivalent" chromatin. Notably, genes that acquire DNA methylation in the soma (muscle) are enriched in transcription factors for alternative cell fates. Remarkably, we find H3K36me3 located in "silent" developmental gene promoters, and not present at the 3' ends of coding regions of genes heavily transcribed during sperm maturation, suggesting different rules for H3K36me3 in iv the germline and soma. We also reveal the chromatin patterns of transposons, rDNA, and tRNAs. Finally, high levels of H3K4me3 and H3K14ac in sperm are correlated with genes activated in embryos prior to the mid-blastula transition (MBT), whereas multivalent genes are correlated with activation at or after MBT. Taken together, gene sets with particular functions in the embryo are packaged by distinctive types of complex and often atypical chromatin in sperm. Bivalent marks, as the chromatin signature of pluripotency, are not persistent and diluted during early synchronous cell division, making them arguable to be heritable epigenetic marks. Studies in early embryos indicate DNA methylation status is the fundamental to confer totipotency and pluripotency. The anticorrelation between DNA methylation profiles and H2A.Z occupancy is conserved from plants to vertebrates. Here, we examined H2afva occupancy in early embryos in zebrafish by ChIP-seq. We found both H2afva level and enrichment remain consistent from sperm to embryos. H2afva is enriched in proximal promoter region in the first nucleosome. Consistent with previous studies, H2afva occupancy is anticorrelated to DNA methylation both in the promoters and outside of promoters. These data suggest H2afva is potentially a heritable epigenetic mark and sets up DNA methylation profiles of totipotency and pluripotency. |
