CANTAC-seq analysis reveals E2f1 and Otx1 coordinate zygotic genome activation in Xenopus tropicalis

Zygotic genome activation is tightly associated with the modulation of chromatin accessibility via maternal transcription factors. Understanding how chromatin accessibility is established and identifying key maternal regulators are crucial to comprehending this process. Here, by developing CANTAC-seq, we generate a genome-wide map of accessible chromatin of early Xenopus tropicalis embryos and find that the open chromatin landscape is progressively established at cis-regulatory elements during zygotic genome activation. Based on the motif analysis and perturbation experiments, we demonstrate that E2f1 maintains a repressive chromatin environment and inhibits zygotic gene transcription before the mid-blastula transition. Moreover, we identify that Otx1, another maternal transcriptional activator, coordinates with E2f1 in regulating chromatin accessibility and zygotic genome activation. Together, E2f1 and Otx1 determine the timely expression of a subset of genes required for zygotic gene transcription and germ layer differentiation.