Extended Data Fig. 5: CTCFY226A/F228A mutation has little effect on CTCF levels at CTCF sites. | Nature

Extended Data Fig. 5: CTCFY226A/F228A mutation has little effect on CTCF levels at CTCF sites.

From: The structural basis for cohesin–CTCF-anchored loops

Extended Data Fig. 5

a, Hi-C contact matrix of region chromosome 16: 77000000–78300000 at 10-kb resolution for the wild-type cell line (bottom triangles) and the CTCFY226A/F228A cell line (top triangles). CTCF sites are depicted below; those selected for qPCR are shown in colour. Red triangles indicate sites with a forward motif and blue triangles indicate sites with a reverse motif. The numbers underneath indicate the qPCR primer pairs shown in b. Primer pair 11 (indicated with *) is at a locus devoid of SCC1 and CTCF. b, ChIP–qPCR analysis of SCC1 (cohesin) enrichment at the aforementioned CTCF sites and control locus (*) in wild-type and CTCFY226A/F228A cells. The mean of three independent ChIP experiments is shown with the s.d. c, ChIP–seq tracks for SCC1 and CTCF at region chromosome 16: 77000000–78300000 in wild-type and CTCFY226A/F228A cells. The loci used for ChIP–qPCR analysis are indicated below the SCC1 ChIP–seq tracks. RPKM, reads per kilobase per million reads. d, ChIP–qPCR analysis of CTCF abundance at loci 1–7, as described in Fig. 3d. Analysis includes IgG as a control. The mean of two independent ChIP experiments is shown. Details of replicates are given in the Methods. e, ChIP–qPCR analysis of CTCF abundance at loci 8–12, as described in Extended Data Fig. 4a. Analysis includes IgG as a control. The mean of two independent ChIP experiments is shown. Details of replicates are given in the extended methods.

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