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

Huanhuan Cui (), Weizheng Liang, Zhaoying Shi, Luming Zhang, Guipeng Li, Rui Chen, Chi Tian, Diwen Gan, Xinyao Shi, Zhiyuan Sun, Qionghua Zhu, Liang Fang, Hongda Huang, Yuhui Hu, Yonglong Chen and Wei Chen ()
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Huanhuan Cui: Southern University of Science and Technology
Weizheng Liang: Southern University of Science and Technology
Zhaoying Shi: Southern University of Science and Technology
Luming Zhang: Southern University of Science and Technology
Guipeng Li: Southern University of Science and Technology
Rui Chen: Southern University of Science and Technology
Chi Tian: Southern University of Science and Technology
Diwen Gan: Southern University of Science and Technology
Xinyao Shi: Southern University of Science and Technology
Zhiyuan Sun: Southern University of Science and Technology
Qionghua Zhu: Southern University of Science and Technology
Liang Fang: Southern University of Science and Technology
Hongda Huang: Southern University of Science and Technology
Yuhui Hu: Southern University of Science and Technology
Yonglong Chen: Southern University of Science and Technology
Wei Chen: Southern University of Science and Technology

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: Abstract 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.

Date: 2025
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DOI: 10.1038/s41467-025-65146-8

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