Background: In animals, initial embryonic development proceeds according to maternal instructions deposited in the egg prior to fertilisation in the form of mRNA and protein; the zygotic genome is transcriptionally silent during this time. At a certain point, the genome of the embryo becomes active during a phenomenon known as zygotic genome activation (ZGA): the “coming of age” of the embryo. The mechanisms of ZGA are as yet unclear. We hypothesise that it is the formation of a transcriptionally competent 3D genome that allows the embryo to initiate transcription and to take charge of its own development. Zebrafish are an excellent tool for asking such fundamental questions about developmental biology; in particular, the rapid development of zebrafish embryos allows for high throughput experiments that would be unfeasible in other model organisms.
Methods: We have performed ATAC-seq in zebrafish embryos across ZGA in an effort to investigate the accessibility of the chromatin. We also knocked down Rad21 (a subunit of the structural protein cohesin) to observe the role of cohesin in establishing or maintaining chromatin accessibility.
Results: We found that in both wild-type and rad21 knockdown conditions, chromatin accessibility increased slightly during ZGA and markedly post-ZGA. This increase in chromatin accessibility is supported by RNA-seq data from our lab as well as previous literature in other organisms, and alongside a ChIP-seq dataset for Rad21 suggests cohesin plays an important role during ZGA.