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Updated: Nov 12, 2025
Methyl-binding DNA capture Sequencing for Patient Tissues
Published on: October 31, 2016
CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer
Musaddeque Ahmed1, Fraser Soares1, Ji-Han Xia2
1Princess Margaret Cancer Center/University Health Network, Toronto, ON, Canada.
Abstract:
Prostate cancer (PCa) risk-associated SNPs are enriched in noncoding cis-regulatory elements (rCREs), yet their modi operandi and clinical impact remain elusive. Here, we perform CRISPRi screens of 260 rCREs in PCa cell lines. We find that rCREs harboring high risk SNPs are more essential for cell proliferation and H3K27ac occupancy is a strong indicator of essentiality. We also show that cell-line-specific essential rCREs are enriched in the 8q24.21 region, with the rs11986220-containing rCRE regulating MYC and PVT1 expression, cell proliferation and tumorigenesis in a cell-line-specific manner, depending on DNA methylation-orchestrated occupancy of a CTCF binding site in between this rCRE and the MYC promoter. We demonstrate that CTCF deposition at this site as measured by DNA methylation level is highly variable in prostate specimens, and observe the MYC eQTL in the 8q24.21 locus in individuals with low CTCF binding. Together our findings highlight a causal mechanism synergistically driven by a risk SNP and DNA methylation-mediated 3D genome architecture, advocating for the integration of genetics and epigenetics in assessing risks conferred by genetic predispositions.
Insights
Prostate cancer risk SNPs in regulatory elements impact cell growth. DNA methylation and CTCF binding at a specific site control MYC expression, influencing tumor development.
Area of Science:
- Genomics
- Epigenetics
- Cancer Biology
Background:
- Prostate cancer (PCa) risk-associated single nucleotide polymorphisms (SNPs) are found in cis-regulatory elements (rCREs).
- The functional roles and clinical significance of these rCREs are not fully understood.
Purpose of the Study:
- To investigate the functional impact of rCREs harboring PCa risk SNPs.
- To elucidate the mechanisms by which these elements influence gene expression and tumorigenesis.
Main Methods:
- CRISPR interference (CRISPRi) screens were conducted on 260 rCREs in PCa cell lines.
- Histone modification (H3K27ac) occupancy and DNA methylation levels were analyzed.
- Expression quantitative trait locus (eQTL) analysis was performed on prostate specimens.
Main Results:
- rCREs with high-risk SNPs are crucial for PCa cell proliferation, with H3K27ac occupancy indicating essentiality.
- Cell-line-specific essential rCREs in the 8q24.21 region, including rs11986220, regulate MYC and PVT1 expression.
- DNA methylation-controlled CTCF binding at a specific site mediates the cell-line-specific regulation of MYC by the rs11986220-containing rCRE.
- CTCT binding variability in prostate specimens correlates with MYC eQTLs in individuals with low CTCF binding.
Conclusions:
- A causal mechanism involving risk SNPs and DNA methylation-driven 3D genome architecture drives PCa.
- Integrating genetic and epigenetic data is crucial for assessing risks associated with genetic predispositions in prostate cancer.
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