Fig. 1: MNase CTCF HiChIP data contains short (~<80 bp) CTCF-protected fragments and longer (~>120 bp) nucleosome-protected fragments.

A Schematic illustrating relationship between short fragments and observed ligations. B Schematic illustrating how the fragment length results from MNase cutting around bound proteins of different sizes. Created in BioRender. Aryee, M. (2025) https://BioRender.com/g98u240C Fragment length distribution for all fragments (top plot) and fragments overlapping occupied CTCF motifs (lower plot). Occupied CTCF motifs are defined here as CTCF motifs within 30 bp of a CTCF ChIP-seq peak summit. D Bar plot quantifying the frequency of different fragment lengths genome-wide and how often each fragment length group overlaps an occupied CTCF motif. Occupied CTCF motifs are defined here as CTCF motifs within 30 bp of a CTCF ChIP-seq peak summit. E Fragment coverage metaplot +/− 500 bp around CTCF binding sites. Schematic below the coverage metaplot illustrates the likely proteins producing these peaks. Schematic created in BioRender. Aryee, M. (2025) https://BioRender.com/g98u240 (F) Plot (E) stratified by fragment length.