CTCF-RNA interactions orchestrate cell-specific chromatin loop organization

• DOI: 10.1101/2025.03.19.643339
• Publication Date: 2025-03-22T02:48:16Z
• Authors: Kimberly Lucero; Sungwook Han; Pin-Yao Huang; Xiang Qiu; Esteban O. Mazzoni; Danny Reinberg

SUMMARYCCCTC-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,PodxlandGrb10, disrupted chromatin loopsin 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.HIGHLIGHTSCTCF 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 loopsin cis.GRAPHICAL ABSTRACT