CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

Genome Biol. 2018 Oct 8;19(1):160. doi: 10.1186/s13059-018-1531-0.


Background: Recent genome-wide association studies (GWAS) have identified more than 100 loci associated with increased risk of prostate cancer, most of which are in non-coding regions of the genome. Understanding the function of these non-coding risk loci is critical to elucidate the genetic susceptibility to prostate cancer.

Results: We generate genome-wide regulatory element maps and performed genome-wide chromosome confirmation capture assays (in situ Hi-C) in normal and tumorigenic prostate cells. Using this information, we annotate the regulatory potential of 2,181 fine-mapped prostate cancer risk-associated SNPs and predict a set of target genes that are regulated by prostate cancer risk-related H3K27Ac-mediated loops. We next identify prostate cancer risk-associated CTCF sites involved in long-range chromatin loops. We use CRISPR-mediated deletion to remove prostate cancer risk-associated CTCF anchor regions and the CTCF anchor regions looped to the prostate cancer risk-associated CTCF sites, and we observe up to 100-fold increases in expression of genes within the loops when the prostate cancer risk-associated CTCF anchor regions are deleted.

Conclusions: We identify GWAS risk loci involved in long-range loops that function to repress gene expression within chromatin loops. Our studies provide new insights into the genetic susceptibility to prostate cancer.

Keywords: CRISPR; CTCF; Chromatin looping; GWAS SNPs; Prostate cancer.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Acetylation
  • CCCTC-Binding Factor / metabolism*
  • Cell Line, Tumor
  • Chromatin / metabolism*
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
  • Enhancer Elements, Genetic / genetics
  • Gene Deletion*
  • Histones / metabolism
  • Humans
  • Lysine / metabolism
  • Male
  • Polymorphism, Single Nucleotide / genetics
  • Prostatic Neoplasms / genetics*
  • Risk Factors
  • Small-Conductance Calcium-Activated Potassium Channels / genetics
  • Up-Regulation / genetics


  • CCCTC-Binding Factor
  • Chromatin
  • Histones
  • KCNN3 protein, human
  • Small-Conductance Calcium-Activated Potassium Channels
  • Lysine