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3C-MTS technology identifies distant genomic interactions made by a cancer risk locus

Du M, Yuan T, et al. (2015) Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome. Hum Mol Genet, 24 (1):154–166.

Citation summary: Chromosome conformation capture-based multiple target sequencing (3C-MTS) technology is used to obtain a genome-wide view of regions that physically interact with the prostate cancer risk locus 8q24. This method combines a 3C assay with multi-target capture sequencing using xGen Lockdown Probes.

Aug 28, 2015

Background

Genetic variants of the 8q24 locus have been shown to increase the risk of prostate cancer (PC) because of their potential to influence distant target genes. Technical barriers in the past have limited studies of 8q24 to its interactions with 2 known proto-oncogenes, MYC and PVT1, which are both found intra-chromosomally on chromosome 8. Technological advances, however, now allow a region of interest to undergo a high-resolution survey where interaction frequencies with other loci across the entire genome can be seen. In this paper, the authors report on use of genome-wide capture technology to further understand the role of 8q24 in PC risk.

Experiment

Du et al. used chromosome conformation capture-based multiple target sequencing (3C-MTS) technology to obtain a genome-wide view of regions that physically interact with the 8q24 risk locus. The method, which combines a 3C assay with multi-target capture sequencing, was applied to 6 distinct cell lines, including 3 prostate-derived lines that were known to be cancerous. DNA from each line was cross-linked, digested, and ligated to create a 3C library, and xGen® Lockdown® Probes and qPCR were used to target and quantify specific regions of DNA upstream and downstream of EcoRI sites.

Results and conclusion

In all 6 cell lines, multiple gene regions were seen to interact with the 8q24 risk locus, including both intra-chromosomal and inter-chromosomal regions. In particular, the MYC locus commonly interacted with the 8q24 locus, which supports previous genetic research on factors influencing PC risk. Another common interacting region was 3q13, which contains the protein-coding CD96 gene. Interestingly, the 3 cancerous cell lines revealed much higher interaction frequencies with 3q13 when compared to the non-malignant lines. Other frequent interactions with the 8q24 locus include known members of β-catenin and Wnt signaling pathways. These findings support the 8q24 locus as a regulatory hub that is highly involved in cell proliferation mechanisms, and validate 3C-MTS technology as a powerful tool for surveying genome-wide interactions between loci.

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