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. Author manuscript; available in PMC: 2019 Mar 9.
Published in final edited form as: Science. 2018 Mar 9;359(6380):1166–1170. doi: 10.1126/science.aan5480

Fig. 4. Inherited hemiCpGs flanking CTCF/cohesin sites may regulate chromatin interactions.

Fig. 4.

(A) Frequency of motif or opposite strand-methylated (same me or oppo me) intraCpGshemi around oriented CTCF motifs co-occupied by CTCF/SMC1A from the two nascent DNA duplexes. Frequency of hairpinCpGhemi from CTCF ChIP-hairpinBS-seq is also shown. (B) All CTCF motifs co-occupied by CTCF/SMC1A in pulse were ranked by their Hemi Index. ΔmC of CpGs from the two nascent DNA duplexes, and reads per million (RPM) for CTCF and SMC1A nasChIP-seq within al kb window surrounding the motifs are shown. Black in the ΔmC heatmaps represents missing data points. (C) All hemiCpGs (ΔmC≥67% or ≤−67%) from two flanking regions in (B) were retrieved. Methylation frequency of the 2 Cs in the other dyad in pulse (left) or the same dyad in chase (right) are shown. ***,_p<0.001. NS, not significant. (D) The Hemi Index of CTCF motifs showing HI>50 in the pooled data were compared between two dyads, from pulse to chase, and across 5 passages. (E) Occupancy of WT and R133C mutant MeCP2 in WT mESC, and MeCP2 in DNMT1/3A/3B triple KO (TKO) mESCs was profiled around CTCF motifs showing upstream- or downstream-only hemi-methylation in mESCs. (F) The ratio between interaction contacts from Hi-ChIP in WT and DNMT3B-KO HUES64 hESCs emanating from occupied CTCF motifs and extending up to ±l Mb window is shown.