Fig. 3: Asymmetric exchange surrounding CTCF binding sites.

a H3.1 histone occupancy within 2 kb window of annotated CTCF binding regions (number of all sites 83810). Average metaprofile for all the sites (upper panel) and heatmap counts of HA over individual sites (lower panel) are shown. Rows of heatmap are sorted by total H3.1 HA counts in a decreasing manner. Limits of H3.1 HA signals are set to 9. b Exchange levels of histone variants within 2 kb window centered at CTCF sites outside genetic regions and control region shifted 20 kb downstream of annotated CTCF sites (number of CTCF sites outside genetic regions 53917). Data are represented as mean ± SEM. c Schematic representation of CTCF-mediated chromatin loop: Translocation of cohesin on DNA forms nascent chromatin loop until blocked by a pair of CTCF proteins, bound in a convergent orientation. Nucleosomes downstream (+1, +2) and upstream (−1) of CTCF binding sites are shown. d Histone occupancy (metaprofile, upper) and exchange (heatmap, lower) at 2 kb window of CTCF binding regions within non-transcribed intergenic regions (n = 53917). Plots are corrected for motif orientation of CTCF binding sites. Exchange (myc/HA, log2) was calculated for each nucleosome position and represented as heatmap. e Mean histone exchange (myc/HA, log2) calculated for four different nucleosomes surrounding CTCF-occupied and CTCF-unoccupied binding motifs (see Methods for details). Exchange was calculated for 31 bins covering the four nucleosomes. Bars indicate mean values for these 31 bins and error bars represent SEM. f Histone modification profile within DNA loops that show asymmetric H3.3 exchange at +1 and +2 sites. Enrichment (IP/input, log2) of indicated histone marks and RNA Pol II of top 10% H3.3 asymmetrically exchanged CTCF sites are compared to bottom 10% H3.3 asymmetrically exchanged CTCF sites. Fold change surrounding +1, +2, −1, and −2 nucleosome sites are shown. g Histone exchange at CTCF sites overlapping with A-compartment (n = 32606) or B-compartment (n = 11976) as defined in ref. ⁶⁷. Mean exchange (myc/HA, log2) was calculated for 31 bins covering four nucleosomes and further normalized by subtracting to mean exchange (myc/HA, log2) within control regions shifted 20 kb downstream. Error bar denotes SEM. Source data are provided as a Source Data file.