Fig. 1

Multiplexed CAPTURE of locus-specific long-range DNA interactions. a Schematic of multiplexed analysis of locus-specific chromatin interactions by the redesigned CAPTURE2.0 system containing the C-terminal biotin-tagged dCas9 (dCas9-CBio) and sgRNA. Major steps of the CAPTURE-3C-seq method are shown. b Schematic of dCas9-mediated multiplexed capture of the human β-globin LCR. c Genome-wide analysis of dCas9 binding in cells expressing LCR-targeting sgRNAs (sgLCR) or non-targeting sgGal4. Data points for the sgRNA target regions are shown by arrowheads, and the predicted off-targets are shown as red dots. The x- and y-axes denote the log2 mean read counts and the log2 ratio of read counts in sgLCR and sgGal4 samples from N = 2 and 4 CAPTURE-ChIP-seq experiments, respectively. d Genome-wide differential gene expression analysis was performed using RNA-seq in K562 cells expressing dCas9-CBio with sgLCR or wild-type (WT) K562 cells. The β-like globin genes are indicated by colored data points. Pearson correlation coefficient (R) value is shown (N = 2 RNA-seq experiments). e Browser view of LCR-mediated long-range interactions (chr11: 5,222,424-5,323,623; hg19) is shown. Contact profiles including the density map and interactions (or loops) for the dCas9-captured LCR or the resolved individual HS regions are shown. The statistical significance of interactions was determined by the Bayes factor (BF) and indicated by the color scale bars. DHS, ChIP-seq, RNA-seq, ChromHMM, CAPTURE-ChIP-seq (sgLCR), and ChIA-PET (CTCF and RNAPII) data are shown for comparison