Fig. 5

Changes in H3K9me3 occupancy upon CGGBP1 knockdown are tightly linked to motif-free repeat-rich CTCF-binding sites. a All CT (blue, top panel) and KD (red, bottom panel) peaks were classified into motif (no repeats) or repeats (no motifs) using FIMO and RepeatMasker tools. Peaks that could not be unambiguously classified were labeled as "Others" (gray) in both the groups. b Peaks exclusive to CT (blue) or KD (red) were determined in subsets of CT and KD peaks shown in a. Venn diagrams depicting shared or exclusive peaks between 9128 striped blue and 15111 striped red (shown in a) are shown on top in b. Venn diagrams depicting shared or exclusive peaks between 19,801 solid blue and 12,523 solid red (shown in a) are shown on bottom in b. These subsets of peaks help comparing CT and KD for features that vary between them depending on repeat or motif contents exclusively. c, d Frequency distribution of M values representing differences in H3K9me3, H3K27me3 and H3K4me3 read counts (upstream–downstream) 10 kb flanks for the six sets of peaks depicted in b in repeat-rich (no motif) peaks (c) and motif-rich (no repeat) peaks (d). Only H3K9me3 shows weak differences of CT and KD exclusives from common peaks for motif-rich (no repeat) peaks (d). H3K9me3 distribution differs strongly between CT and KD and deviates from common peaks at repeat-rich (no motif) peaks (c) only. e, f The M values depicted in H3K9me3 datasets (d) were separately analyzed for CT and KD to filter out peaks 10 kb flanks of which satisfy two conditions: (i) M value upstream–downstream difference > 1.5 and (ii) the ΔM [(M of KD) − (M of CT)] > 1.5 (e; red and blue spots) or ΔM [(M of CT) − (M of KD)] > 1.5 (f; red and blue spots). g, h Heatmaps of H3K9me3 signals from CT and KD datasets in the peaks corresponding to red-blue peaks in E and F show that there is a clear difference in H3K9me3 signal transitioning exactly at the peak centre where CTCF binding is observed and affected by CGGBP1 in KD. g and h show peaks exhibiting loss and gain of barrier activity, respectively. i, j Genome browser views showing loss of CTCF binding at a representative CT–KD peak that also exhibits loss of H3K9me3 barrier function upon CGGBP1 knockdown (i) [(39 kb region on chr21 starting from approximately 42700 kb), Y-axis represents data ranges 0–50 for CTCF CT, 0–35 CTCF KD, 0–50 for H3K9me3, 0–25 for H3K27me3 and H3K4me3]. A representative KD–CT exclusive peak that shows gain of CTCF binding upon CGGBP1 knockdown also displayed gain of H3K9me3 barrier function (j) [(28 kb region on chr21 starting from approximately 20908 kb], Y-axis represents data ranges 0–100 for CTCF, 0–50 for H3K9me3, 0–25 for H3K27me3 and H3K4me3)