Figure 4: CTCF-binding sites are switched by 17q21 SNPs.
From: 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells
(a) Schematic representation of the 17q21 locus containing CTCF-binding motifs (underlined sequence) that overlap with the linked SNPs rs12936231 (C/G; ZPBP2 site) and rs4065275 (G/A; ORMDL3 site); the asthma-risk SNP is indicated in red, the non-risk SNP in blue. (b) Real-time PCR quantification of DNA sequences, containing the 17q21 linked SNPs rs12936231 (ZPBP2 site) or rs4065275 (ORMDL3 site), after anti-CTCF ChIP of chromatin extracts obtained from polarized TH1, TH2 cells (shown as circles) and primary CD8+ T cells (shown as triangles; see Methods) of donors categorized based on allelic status of SNP overlapping the respective CTCF motif (as shown in a). Data are expressed as fold enrichment relative to an irrelevant background control; data were obtained from four independent experiments and each dot represents data from a single ChIP assay; n=44 assays from 15 subjects (see Methods and Supplementary Fig. 4c,d). (c) Percentage of DNA sequences containing the risk and non-risk SNPs at rs12936231 (ZPBP2 site) or rs4065275 (ORMDL3 site) following Sanger sequencing of DNA obtained following anti-CTCF ChIP assay performed in heterozygous donors shown in b (see Methods and Supplementary Fig. 4b); shown below are nucleotide traces from Sanger sequencing of ChIP and input DNA from a representative experiment. (d) Schematic representation of the switch in CTCF binding introduced by the linked asthma-risk SNPs (rs12936231 and rs4065275) in the 17q21 locus; orange triangles represent binding of CTCF to the preferred allele. ***P<0.001 by Mann–Whitney U-test.
