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Fig. 6 | Genome Biology

Fig. 6

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

Fig. 6

KCNN3 is upregulated upon targeted deletion of the region encompassing the CTCF site near rs12144978. a A blowup of the CTCF peak information, genomic annotation, and looping information for rs12144978 from Fig. 4. b Hi-C chromatin interaction map of the region of chromosome 1 near the rs12144978. The location of the SNP is indicated by the blue line and arrow. The blue circles indicate the high confidence risk loops used in the analysis. c Detailed schematic of the high confidence risk loops in which rs12144978 is involved, as identified by the Hi-C chromatin interaction data. d Shown is the fold-change expression of all genes within a ± 1-Mb region near rs12144978 in the cells deleted for a 1607-bp region encompassing the PCa risk-associated CTCF site (site 1); a volcano plot illustrating the genome-wide analysis of the RNA-seq data can be found in Additional file 1: Figure S2. The yellow X indicates which CTCF site has been deleted. e Shown is the fold-change expression of all genes within a ± 1-Mb region near rs12144978 in the cells deleted for a 913-bp region encompassing CTCF site 3. The yellow X indicates which CTCF site has been deleted

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