| Description |
Cells of the early vertebrate embryo are distinct in their ability to commit into any cell lineage. How the embryo acquires this remarkable plasticity from two terminally differentiated gametes remains largely unknown. The plasticity in early embryo relies on achieving a unique transcriptome, which is regulated at multiple levels - including chromatin accessibility at developmental enhancers and genes. To understand the global landscape of chromatin accessibility during early embryogenesis, we utilized zebrafish embryos and explored three aspects of chromatin regulation. We first focused on the ATPase subunits (Brg1 and Brm) of SWI/SNF complexes, which are important regulators of chromatin accessibility and gene expression in all eukaryotes. To understand where they act in the genome, we profiled the occupancy of Brg1 and Brm by ChIP-seq at three early embryonic stages around the major onset of zygotic genome activation. We observed the occupancy of Brg1 and Brm during early embryogenesis is highly dynamic. The promoters of key pluripotency factors and other developmental transcription factors are robustly occupied by Brg1 and Brm. Interestingly, Brg1, but not Brm, is highly correlated with active histone modifications. However, only Brm commonly occupies gene bodies, which is dependent on transcription elongation. This work suggests SWI/SNF complexes might play important roles during early embryogenesis, and also reveals distinct roles of Brg1 and Brm in early zebrafish development. We then profiled the global landscape of accessible chromatin by ATAC-seq at three embryonic stages, as well as one differentiated tissue, adult liver. The data suggest chromatin accessibility increases during early embryogenesis. Here, 60% of open chromatin regions reside at genic regions and are highly enriched at promoters. Furthermore, many interesting candidate transcription factors are revealed based on motif analyses. Finally, ATAC-seq fragments with length of 120-220bp, together with MNase-seq date are used to profile nucleosome positioning. Our data determines nucleosome positioning during early embryogenesis, also discovered many interesting sequence characteristics involved in nucleosome positioning at various gene features. In summary, this work has extensively investigated the dynamics of chromatin landscape and the role of chromatin remodelers during early zebrafish development, which allow the comprehensive understanding of the regulation during early embryogenesis. |
