Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for proper CTCF function

Abstract

Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and DNA binding of transcription factors, including the insulator protein CTCF. To define which subcomplex mediates these diverse functions, we derived a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits. Individual deletions of subunits of either CERF, RSF, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to drastic reduction in chromatin accessibility and SNF2H ATPase localization around CTCF sites. While this affects adjacent nucleosome occupancy, it only modestly impacts CTCF binding itself. In the absence of accessibility, the structural function of CTCF is nevertheless impaired resulting in lower occupancy of cohesin and cohesin release factor, and reduced physical insulation at these sites, highlighting the need of NURF-mediated remodeling for open chromatin and proper CTCF function. These results separate local CTCF binding from insulator function in nuclear organization and reveal a specific role for NURF in mediating SNF2H localization and chromatin opening at bound CTCF sites. They designate local accessibility as critical for cohesin positioning and establishment of physical insulation.