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

Abstract

BackgroundRecent 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.ResultsWe 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1531-0) contains supplementary material, which is available to authorized users.

Chromatin reprogramming as an adaptation mechanism in advanced prostate cancer

“…This process was regulated by estrogens, which altered the chromatin structure interfering with enhancer-promoters loop formation (Fiorito et al 2016). Like in breast cancer, a role of CTCF in mediating hormone-dependent gene transcription has been shown in PC: Taslim and colleagues found that subsets of androgen-responsive genes were significantly enriched within the same CTCF blocks, suggesting that CTCF is implicated in regulation of a subset of distally located androgen-responsive genes (Taslim et al 2012), which are potentially involved in prostate carcinogenesis (Taslim et al 2012, Guo et al 2018. Collectively, these studies show that the higher-order chromatin conformation is interconnected with local chromatin relaxation and interferes with gene regulation, which may have implications for PC development and progression.…”

Adenine DNA methylation, 3D genome organization and gene expression in the parasiteTrichomonas vaginalis

“…For example, promoter-enhancer loops are strongly associated with gene activation (53) and it has been proposed that the presence of chromatin loops may contribute to the co-regulation of specific block of genes by increasing the local concentration of the transcription machinery, resulting in the formation of structures similar to transcription factories (54). Alternatively, chromatin looping has also been implicated in transcriptional repression in Drosophila (55) and mammals (56). Interestingly, our bioinformatics analysis revealed the presence of active and repressive intervals of varying length flanked by 6mA.…”

A versatile bulk electrotransfection protocol for mouse embryonic fibroblast and iPS cells

“…For the CRISPR/Cas9 study, we modified pX459 plasmid (9151 bp) which encodes a Cas9 protein followed by puromycin antibiotic under CAGGS promoter/enhancer, as well as the gRNA scaffold under the U6 promoter. All gRNAs were synthetized and cloned into the backbone vector based on the Franham protocol (30). Briefly, gRNAs were selected to target Venus promoter or open reading frame (ORF) via CRISPOR software, available online (http://crispor.tefor.net/) (31).…”