Time-resolved succession of epigenetic regulation during early mammalian development

During early mammalian embryonic development, different epigenetic mechanisms undergo dramatic changes; yet how these interconnected epigenetic layers function together to coordinate expression of the genetic code in a spatiotemporal manner remains unknown. Here, we describe a time-resolved study of the hierarchy of epigenetic marks and events, which we used to model transcriptional programs that cannot be understood by investigating steady state. We found that, following fertilization, the re-establishment of accessible chromatin together with transcription factors inherited from oocytes initiates transcription at the 2-cell stage, and then the introduction of active histone modification, H3K4me3, facilitates gene up-regulation at the 4-cell stage, then stabilization of higher-order chromatin structures at the 8-cell stage further enhances transcriptional activity. During the first lineage specification at ICM, transcription activity multifaceted regulation of epigenetic marks. Finally, we quantitatively model the stage succession of different epigenetic marks on transcriptional programs during early embryonic development.