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 ({Delta}ZF1) 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-{Delta}ZF1 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-{Delta}ZF1 expressing NPCs. These findings underscore the inherent importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity. HIGHLIGHTSO_LICTCF loop anchors induced after differentiation are disrupted in the {Delta}ZF1 RNA-binding mutant. C_LIO_LILoop loss in the {Delta}ZF1 mutant is independent of its DNA binding and protein interactions. C_LIO_LIChromatin loop loss is associated with gene dysregulation. C_LIO_LITruncation of cell-specific, CTCF-ZF1-interacting RNAs disrupts chromatin loops in cis. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/643339v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1dad736org.highwire.dtl.DTLVardef@674a5dorg.highwire.dtl.DTLVardef@14345d4org.highwire.dtl.DTLVardef@19d83cb_HPS_FORMAT_FIGEXP M_FIG C_FIG