Dissecting the functional roles of CTCF and CTCF-s in human embryonic stem cells

Hongxin Zhong; Yuli Lu; Jie Zhang; Gongcheng Hu; Guangjin Pan; Hongjie Yao

doi:10.1016/j.jgg.2025.12.007

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Dissecting the functional roles of CTCF and CTCF-s in human embryonic stem cells

doi: 10.1016/j.jgg.2025.12.007

a. Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China;
b. Department of Basic Research, Guangzhou National Laboratory, Guangzhou, Guangdong 510005, China;
c. University of Chinese Academy of Sciences, Beijing 100049, China

Funds:

D Program of Guangzhou (2023B03J1230).

D Program of China (2021YFA1100300), and Key R&

We thank Professor Fei Xavier Chen for sharing the protocol of the TT-seq experiment. The authors also acknowledge the support of Guangzhou Branch of the Supercomputing Center of the Chinese Academy of Sciences. This work was supported by the National Natural Science Foundation of China (32430016, U21A20195), the National Key R&

Received Date: 2024-11-23
Accepted Date: 2025-12-18
Rev Recd Date: 2025-12-18

Available Online: 2025-12-25

Abstract

Abstract

CTCF is a highly conserved zinc finger protein that plays critical roles in transcriptional regulation and three-dimensional (3D) genome organization. An alternative splice isoform of CTCF (CTCF-s), lacking the N-terminal domain and 2.5 zinc fingers, competes with CTCF for genomic occupancy and reduces CTCF-mediated chromatin interactions. However, the functional differences between CTCF and CTCF-s remain unclear. In this study, by using an auxin-inducible degron (AID2) system with doxycycline-inducible transgene expression, we systematically investigate the roles of CTCF and CTCF-s in human embryonic stem cells (hESCs). Acute degradation of endogenous CTCF and CTCF-s, followed by isoform-specific rescue, reveals that CTCF is essential for cell morphology and proliferation, whereas CTCF-s exerts much weaker effects. Genome-wide ChIP-seq and Hi-C analysis uncover distinct binding landscapes for CTCF and CTCF-s, as well as their differential contributions to chromatin conformation. Notably, our data indicate that CTCF-s, like CTCF, could either act as a boundary insulator or bind to gene promoters to modulate expression of a fraction of genes. Overall, our study reveals that CTCF is dominant in regulating chromatin boundary stability and gene regulation, while CTCF-s contributes to a lesser degree.
- CTCF,
- CTCF-s,
- Human embryonic stem cells,
- 3D genome organization

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References(56)

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