The Landscape Of Accessible Chromatin In Mammalian Preimplantation Embryos

In mammals,extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent embryo during preimplantation development.However,the global chromatin configuration and its dynamics in this period remain largely unexplored.Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing(ATAC-seq)approach with CRISPR/Cas9-assisted mitochondrial DNA depletion.We found that despite extensive parental asymmetry in DNA methylomes,the chromatin accessibility between the parental allele is globally comparable after major zygotic genome activation(ZGA).Accessible chromatin in preimplantation embryos is widely shaped by transposable elements and contains putative cis-regulatory elements Unexpectedly,accessible chromatin is also found near the transcription end sites of active genes in early embryo.From the cis-regulatory elements map,we identify the key modulators for lineage specification.Finally,we find that there is little cis-regulatory elements associated open chromatin before major ZGA.In contrast,we observed many loci showing non-canonical,large open chromatin domains over the entire transcribed units in minor ZGA,supporting the presence of an unusually permissive chromatin state.Together,these data reveal the dynamic chromatin regulation during early mammalian embryo development.