Figure 7

Distribution of CTCF at rDNA in human liver cancer cell.

(A) Schematic representation of one human rDNA repeat. ETS: external transcribed spacer; ITS-1/2: internal transcribed spacer-1/2; IGS: intergenic spacer. The coding region, which spans ~0–13.3 kb of the human rDNA repeat, is separated by the non-coding intergenic spacers (IGS). Patterns of CTCF at rDNA in human liver cancer cell line HepG2 were shown below the human rDNA repeat as determined by the analysis of ChIP-seq data. Enrichment P value was calculated using the negative binomial model. (B) Enrichment of CTCF on human rDNA analyzed by ChIP-QPCR. Chromatin from HepG2 cells was cross-linked and immunoprecipitated with CTCF antibody, DNA was analyzed by QPCR with different sets of primers indicated in (A). The percentage of DNA associated with anti-CTCF antibody was calculated relative to the DNA from ChIP input. Values are represented by means ± SD from three independent ChIP experiments, each experiment was tested by at least three independent QPCR reactions. Student’s t-test was performed between human liver cancer cell (LC Control) and normal liver cell (CC Control). (C)Depletion of UBF leads to no change of CTCF at human rDNA. ChIP-QPCR analysis of different regions of rDNA in HepG2 cells transfected with control or UBF siRNA using antibodies against CTCF. The ratio of rDNA occupancy between UBF knockdown cells and control cells was calculated for each antibody. Student’s t-test was performed between cells transfected with or without UBF siRNA.