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bioRxiv · 10.64898/2026.03.17.712290

A dual role for CTCF in development

Alonso Saiz, N.·Martinovic, M.·Rubio, M.·Samal, P.·Giselbrecht, S.·Braccioli, L.·de Wit, E.
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Abstract

CTCF is an essential DNA binding protein whose absence leads to embryonic lethality. CTCF is primarily known for its role in 3D genome organization where its N-terminal domain interacts with cohesin to anchor chromatin loops. How CTCF facilitates proper embryonic development remains unclear, necessitating temporal control to resolve its stage-specific functions. By combining gastruloids, an in vitro model of embryonic development, with a degron system to rapidly deplete CTCF at defined timepoints, we show that early CTCF depletion impairs early gastruloid morphogenesis. Surprisingly, ATAC-seq and time-resolved RNA-seq revealed that differentiation was unaffected. CTCF binding is strongly enriched at promoters of downregulated genes. Re-expression of a CTCF variant with an N-terminal truncation, incapable of looping, was sufficient to rescue the expression of CTCF-promoter bound genes and the defects in morphogenesis. However, extended culture (up to 168 hours) of gastruloids reconstituted with N-terminal truncated CTCF led to their collapse. Our work shows that CTCF has a dual function in early mammalian development: at early stages CTCF regulates developmentally important genes through promoter binding, while at later stages its looping function is required for correct development. HighlightsO_LICTCF is essential for gastruloid morphogenesis but dispensable for cell differentiation C_LIO_LICTCF activates genes through promoter binding C_LIO_LICTCF promoter target regulation drives in vitro gastrulation C_LIO_LIPost-gastrulation development in vitro is driven by CTCFs looping function C_LI

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Alonso Saiz, N., Martinovic, M., Rubio, M., Samal, P., Giselbrecht, S., Braccioli, L., de Wit, E.. 2026-03-18. A dual role for CTCF in development. https://doi.org/10.64898/2026.03.17.712290

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