Fig. 4: Cohesin footprint observed in MNase HiChIP and experimentally confirmed in mESC RCMC.

A High and low CTCF occupancy motifs. For each occupancy level, CTCF ChIP-seq and all fragments overlapping the CTCF motif are depicted, along with the corresponding fragment length histogram. B The fraction of reads overlapping a CBS (+) that are short (<120 bp) strongly correlates with the strength of its CTCF ChIP-seq signal. The fraction of short reads (<120 bp) was calculated for each CBS, plotted in a density, and colored by absence of CTCF ChIP-seq peak or CTCF ChIP-seq signalValue quartile. C K562 CTCF MNase HiChIP 2D density for short (<120 bp) left fragments overlapping CAMEL-identified CBS (+) (N = 10,906 CBS). The fragment start and fragment end are aligned relative to the start of the 35 bp CTCF motif (MA1930.1), so that “0” in the plots corresponds to the start of the 35 bp CTCF motif. D Annotated 35 bp JASPAR CTCF motif (MA1930.1). E mESC RCMC 2D density for short (<120 bp) left fragments overlapping CTCF motifs within 30 bp of a mESC CTCF ChIP-seq peak (N = 65 CBS). The fragment start and fragment end are aligned relative to the start of the 35 bp CTCF motif (MA1930.1), so that “0” in the plots corresponds to the start of the 35 bp CTCF motif. F Schematic illustrating the most prevalent fragment type observed in the mESC RCMC perturbations shown in (E). G Schematic showing the three classified types of fragments relative to the location of the CTCF motif. The interaction partners of these three fragment types are graphed in (H, I). H Short TF-sized fragments (<120 bp) with an extended fragment end have a noticeably larger bump in density of long range interactions (>10 kb) compared to TF-sized short fragments without an extended fragment end and nucleosome-sized long fragments (>120 bp). I P(S) curve for fragments depicted in (H).