CTCF Mediates the Cell-Type Specific Spatial Organization of the Kcnq5 Locus and the Local Gene Regulation (original) (raw)
Figure 2
The cell-type specific binding of CTCF and cohesin binding sites and the spatial organization of the kcnq5 locus.
(A) A schematic representation of the chromatin fragments of the kcnq5 locus for ChIP and 3C assays. The eight Hind III-digested chromatin fragments for the 3C assay were aligned using the UCSC Genome Browser, each of which encompassed a potential CTCF binding site. The 3C primers were designed to correspond to the sequences near the downstream sticky ends of the 3C fragments and named p1 to p8 according to their position on the gene locus. The primer pairs for ChIP assay were designed to span each potential CTCF binding sites. Real-Time quantitative PCR analyzed the DNA fragments enriched by anti-CTCF and Rad21 ChIP assays with (B) MCF-7 cells and (C) Jurkat cells (*: the relative enrichment was 82). The independent quantitative PCR amplification efficiency was normalized by the input template. Error bars represent mean ± s.d. (n = 3). (D) 3C quantitative PCR assay detected the interaction frequencies between the chromatin fragments of the kcnq5 gene locus in MCF-7 and Jurkat cells (the relative interaction frequencies, ▴: 840 and ▴▴: 770). The amplification efficiencies of the independent PCR reactions were normalized with respect to the control template. Error bars represent mean ± s.d. (n = 3).