Project description:To be able to fully comprehend the contribution of the epigenome to embryonic development, it is important to understand how various components of the epigenome evolved. To date, a number of studies have thoroughly described various epigenetic mechanisms in both vertebrates and invertebrates, however there is currently a lack of high resolution epigenomic data corresponding to animals that form the invertebrate-vertebrate boundary. To that end, we have sequenced the genome of the European amphioxus (Branchiostoma lanceolatum) and explored various layers of its epigenome. Our whole genome bisulfite sequencing (MethylC-seq) approach revealed that amphioxus displays invertebrate-like, mosaic DNA methylation patterns. Nevertheless, we found significant DNA methylation remodeling events taking place during tissue differentiation, mostly consisting of developmental hypomethylation. This developmental loss of DNA methylation temporally coincides with the activation of the Tet protein orthologue in the amphioxus genome, suggestive of active demethylation. Furthermore, comparisons with chromatin accessibility data (ATAC-seq) demonstrate that this demethylation event affects cis regulatory elements, as previously described in vertebrates. Altogether, our study provides a rich developmental resource for studying epigenome evolution and demonstrates for the first time the existence of embryonic DNA methylation remodeling in an invertebrate chordate.
Project description:DNA methylation and hydroxymethylation are extensively reprogrammed in mammalian early embryogenesis. However, a comprehensive picture of DNA hydroxymethylation map across early embryo stages is lacking. Here, we develop “schmC-CATCH” (single-cell 5hmC chemical-assisted C-to-T conversion-enabled sequencing) to obtain quantitative, genome-wide landscape of the base-resolution DNA hydroxymethylome in mouse gametes and pre-implantation embryos from one-cell (PN1-PN5) to blastocyst stages. We revealed the dynamics of DNA hydroxymethylation and observed dramatically different 5hmC patterns on the paternal and maternal genomes. We found hotspots of DNA hydroxymethylation during mouse early embryo development, which are highly associated with young retroelements including LINE1. 5hmC is also associated with regulatory elements, indicating a potential epigenetic function during early embryogenesis. In addition, 5hmC is asymmetrically distributed at the chromosome level and can be used to track the cell and strand lineages during the first two embryo cleavages. Collectively, our work reveals the dynamics of active DNA demethylation during mouse pre-implantation development and provides an important resource for functional studies of epigenetic reprogramming in single cells.
Project description:The effects of ethanol on developmental gene expression in sea urchins is compared to controls at three time points during gastrulation.