Fig. 2

Multiplexed CAPTURE of erythroid super-enhancers. a Schematic of the multiplexed analysis of erythroid SEs. SEs were identified by ROSE [37] using H3K27ac ChIP-seq signal in K562 cells. Schematic of sgRNA design is shown. Pie charts on the left show the distribution of the captured SEs and constituent enhancers at intragenic, intergenic, or both regions. Pie charts on the right show the numbers and percentages of captured SEs and constituent enhancers (green color). b Genome-wide analysis of dCas9 binding in cells expressing SE-targeting sgRNAs (sgSE) or non-targeting sgGal4. Data points for the sgRNA captured SEs are shown as green. The x- and y-axes denote the log2 mean read counts and the log2 ratio of read counts in sgSE and sgGal4 samples from N = 2 and 4 CAPTURE-ChIP-seq experiments, respectively. c Genome-wide differential gene expression analysis was performed using RNA-seq in K562 cells expressing dCas9-CBio with sgSE or WT K562 cells. Data points for SE target genes and other genes are shown as red and gray, respectively. Pearson correlation coefficient (R) value is shown (N = 2 RNA-seq experiments). d Analysis of SE-mediated long-range interactions by categorizing all interactions into SEs to gene promoters (SE-P), SEs to gene bodies (SE-G), and SEs to other genomic regions (SE-O). Schematic of SE-mediated interactions is shown on the top. The interaction frequency was calculated by the normalized PETs per kilobase of captured DNA sequences. Boxes show the median of the data and quartiles, and whiskers extend to 1.5× of the interquartile range. P values were calculated by a two-sided Kolmogorov-Smirnov (K-S) test. e Pie chart shows the fractions of the captured SE-mediated interactions between SEs and gene targets. f A representative locus is shown for the single SE to single gene interactions (SE137). Contact profiles including the density map and interactions for the dCas9-captured SE region (red bar) are shown. The statistical significance of interactions was determined by the Bayes factor (BF) and indicated by the color scale bars. DHS, ChIP-seq, ChromHMM, ChIA-PET (CTCF and RNAPII), and in situ Hi-C data are shown for comparison. g A representative locus is shown for the single SE to multiple genes (SE43). h A representative locus is shown for the multiple SEs to multiple genes (SE41 and SE42)