Characterization of the distribution and dynamics of chromatin states in the C. elegans germ line reveals substantial H3K4me3 remodeling during oogenesis
Chromatin organization in the C. elegans germ line is tightly regulated and critical for germ cell differentiation. While certain germline epigenetic regulatory mechanisms have been identified, how they influence chromatin structure and ultimately gene expression remains unclear, in part because most genomic studies have focused on data collected from whole worms. We therefore analyzed publicly available histone modification and chromatin accessibility data from isolated undifferentiated germ nuclei to define chromatin states. We then correlated these states with overall transcript abundance, spatio-temporal expression patterns, and the function of small RNA pathways. Because the essential role of the germ line is to transmit genetic information to the next generation and establish gene expression in the early embryo, we compared epigenetic and transcriptomic profiles from undifferentiated germ cells, oocytes, and embryos to define the epigenetic changes during this developmental transition. The active histone modification H3K4me3 exhibits particularly dynamic remodeling as germ cells differentiate into oocytes, with implications for establishing transcriptional activation of essential genes during early embryogenesis. Our results highlight the dynamism of the chromatin landscape in germ cells, and provide a resource for future investigation into epigenetic regulatory mechanisms. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K4me3 of early embryos in C. elegans.