Quantitative Chromosome Conformation Capture (3C-qPCR)

Abstract

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Transcriptional activation of the Myc gene by glucose in β-cells requires a ChREBP-dependent 3-D chromatin interaction between the Myc and Pvt1 genes

“…3C was performed as described in [ 64 ]. Briefly, 10ˆ6 INS-1 cells were transduced with 150 MOI of the indicated adenovirus and cultured in the indicated concentrations of glucose.…”

DLK1/DIO3 locus upregulation by a β-catenin-dependent enhancer drives cell proliferation and liver tumorigenesis

“…and Rebouissou et al. 26 , 54 and conducted on 5 million nuclei isolated from hepatocytes lysed in homogenization buffer with an Ultra-Turrax during 20 min on ice and centrifuged for 1 h at 20,000 × g . The 3C assays were performed with EcoRI digestion, product ligation, and secondary XbaI digestion (N ≥ 3).…”

Transcriptional memory is conferred by combined heritable maintenance and local removal of selective chromatin modifications

“…3C-qPCR was performed according to the published protocol 54 with the following specifications. 0.8-1 x 10^6 cells were used per sample.…”

“…For RT-qPCR assays, each final 3C sample was diluted to 25 ng DNA per reaction. Ct values were normalized according to the published protocol 54 with primer efficiency determined computationally from amplification efficiency per PCR cycle using LinReg software 51 and amplification of E2 or CH-C baits within digested fragment set as a loading control. The oligonucleotides used for RT-qPCR are listed in Table S1.…”