Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF

Abstract

Catalytic activity of the imitation switch (ISWI) family of remodelers is critical for nucleosomal organization and DNA binding of certain transcription factors, including the insulator protein CTCF. Here we define the contribution of individual subcomplexes by deriving 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 a strong reduction in chromatin accessibility and SNF2H ATPase localization around CTCF sites. This affects adjacent nucleosome occupancy and CTCF binding. At a group of sites with reduced chromatin accessibility, CTCF binding persists but cohesin occupancy is reduced, resulting in decreased insulation. These results suggest that CTCF binding can be separated from its function as an insulator in nuclear organization and identify a specific role for NURF in mediating SNF2H localization and chromatin opening at bound CTCF sites.

Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2

“…In contrast, flanking regions around strong CTCF sites displayed sequence preferences 2 to 13bp downstream and -15 to -7bp upstream of the core motif, though these were more subtle than the core motif itself (Fig 3E). Influential flanking sequences for genome folding, as predicted by AkitaV2, aligned well with previously documented CTCF binding preferences upstream and/or downstream of the core motif derived from ChIP-seq, MNase-seq, and ChIP-exo [35][36][37][38][39][40]. The sequence preferences we observed differed from those reported by [15], possibly due to a limited number of experimentally tested sites.…”

“…We also observed an initial dip in insertion score at an inter-motif distance of ~170bp, consistent across all four orientations (Fig 6D). Interestingly, this is close to the nucleosome repeat length estimated from MNase-seq [38], and strong CTCF sites are often flanked by arrays of phased nucleosomes [47,48]. The profiles for tandem left and tandem right sites are closely aligned, confirming the model's strand independence.…”

“…Although lower information content than the core motif, strong sites displayed sequence preferences both upstream and downstream of the core. While not pronounced enough to be readily extracted by motif-discovery algorithms, the flanking sequences identified by AkitaV2 show similarities to those reported as important for CTCF binding and DNA accessibility [35][36][37][38][39][40]50]. Similarly to us, [39] and [38] used neural network models to extract sequence preferences around CTCF sites, albeit starting from predicted DNA accessibility instead of predicted genome folding.…”

“…While not pronounced enough to be readily extracted by motif-discovery algorithms, the flanking sequences identified by AkitaV2 show similarities to those reported as important for CTCF binding and DNA accessibility [35][36][37][38][39][40]50]. Similarly to us, [39] and [38] used neural network models to extract sequence preferences around CTCF sites, albeit starting from predicted DNA accessibility instead of predicted genome folding. Differences with [15] likely come from limitations to the number of sites that could be experimentally assayed.…”