CTCF-RNA interactions orchestrate cell-specific chromatin loop organization.

: CCCTC-binding factor (CTCF) is essential for chromatin organization. CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA-binding region (ΔZF1) disrupts chromatin loops in mouse embryonic stem cells (ESCs). However, the functional significance of CTCF-ZF1 RNA interactions during cell differentiation is unknown. Using an ESC-to-neural progenitor cell (NPC) differentiation model, we show that CTCF-ZF1 is crucial for maintaining cell-type-specific chromatin loops. Expression of CTCF-ΔZF1 leads to disrupted loops and dysregulation of genes within these loops, particularly those involved in neuronal development and function. We identified NPC-specific, CTCF-ZF1 interacting RNAs. Truncation of two such coding RNAs, Podxl and Grb10 , disrupted chromatin loops in cis , similar to the disruption seen in CTCF-ΔZF1 expressing NPCs. These findings underscore the inherent importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity.

Conclusions: CTCF loop anchors induced after differentiation are disrupted in the ΔZF1 RNA-binding mutant.Loop loss in the ΔZF1 mutant is independent of its DNA binding and protein interactions.Chromatin loop loss is associated with gene dysregulation. Truncation of cell-specific, CTCF-ZF1-interacting RNAs disrupts chromatin loops in cis . null