Wen Wang1,2,8, Rui Gao1,8, Dongxu Yang1,2,8, Mingli Ma1,2,8, Ruge Zang1, Xiangxiu Wang3, Chuan Chen4, Xiaochen Kou1, Yanhong Zhao1, Jiayu Chen1,5, Xuelian Liu2,6,7, Jiaxu Lu2, Ben Xu1, Juntao Liu2, Yanxin Huang1, Chaoqun Chen2, Hong Wang1, Shaorong Gao1,2,5, Yong Zhang2,5 and Yawei Gao2,5 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; 2State Key Laboratory of Cardiology and Medical Innovation Center, Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; 3Key Laboratory of Biorheological and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Modern Life Science Experiment Teaching Center at Bioengineering College of Chongqing University, Chongqing 400030, China; 4Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China; 5Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai 200120, China; 6Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; 7University of Chinese Academy of Sciences, Beijing 100049, China Corresponding authors: gaoshaorongtongji.edu.cn, gaoyaweitongji.edu.cn, yzhangtongji.edu.cn

↵8 These authors contributed equally to this work.

Abstract

CTCF is crucial for chromatin structure and transcription regulation in early embryonic development. However, the kinetics of CTCF chromatin occupation in preimplantation embryos have remained unclear. In this study, we used CUT&RUN technology to investigate CTCF occupancy in mouse preimplantation development. Our findings revealed that CTCF begins binding to the genome prior to zygotic genome activation (ZGA), with a preference for CTCF-anchored chromatin loops. Although the majority of CTCF occupancy is consistently maintained, we identified a specific set of binding sites enriched in the mouse-specific short interspersed element (SINE) family B2 that are restricted to the cleavage stages. Notably, we discovered that the neuroprotective protein ADNP counteracts the stable association of CTCF at SINE B2-derived CTCF-binding sites. Knockout of Adnp in the zygote led to impaired CTCF binding signal recovery, failed deposition of H3K9me3, and transcriptional derepression of SINE B2 during the morula-to-blastocyst transition, which further led to unfaithful cell differentiation in embryos around implantation. Our analysis highlights an ADNP-dependent restriction of CTCF binding during cell differentiation in preimplantation embryos. Furthermore, our findings shed light on the functional importance of transposable elements (TEs) in promoting genetic innovation and actively shaping the early embryo developmental process specific to mammals.

Received September 18, 2023. Accepted February 20, 2024.