Fig. 4

Analysis of promoter-centric chromatin interactions by multiplexed CAPTURE. a Schematic of multiplexed CAPTURE of promoter-centric interactions during erythroid differentiation of G1ER cells using sgRNAs targeting 22 activated (sgAct) or 20 repressed (sgRep) promoters. RNA-seq, ATAC-seq, ChIP-seq (H3K27ac and H3K4me3), and CAPTURE-3C-seq of promoter-centric interactions were performed in undifferentiated (0 h) and differentiated (2, 6, 12, and 24 h) G1ER cells. b Genome-wide gene expression analysis of cells expressing target-specific sgRNAs (sgAct or sgRep) in undifferentiated (0 h) and differentiated (24 h) G1ER cells. Data points for the sgRNA-targeted activated or repressed promoters are shown as green and red, respectively. The x- and y-axes denote the log2 read counts in sgAct and sgRep samples from N = 3 RNA-seq experiments, respectively. c Differential gene expression analysis in G1ER cells expressing dCas9-CBio with sgAct, sgRep, or non-targeting sgGal4. Pearson correlation coefficient (R) values are shown for pair-wise comparisons (N = 3 RNA-seq experiments). d Pie charts show the numbers and percentages of captured activated or repressed promoters (green color). e A representative locus is shown for the activated promoter (Mafk)-mediated chromatin interactions during erythroid differentiation. Contact profiles including the density map and interactions for the dCas9-captured region (blue bar) and interacting CREs (red bar) are shown. The statistical significance of interactions by the Bayes factor (BF) is indicated by the color scale bars. The locations of the annotated Mafk TSS, Tmem184a TSS, and candidate enhancers are shown on the bottom. Numbers represent the distances to the Mafk TSS (+ 1). Two independent experiments were performed for RNA-seq, ATAC-seq, ChIP-seq, and multiplexed CAPTURE-3C-seq in G1ER cells at varying time points of erythroid differentiation, and the replicates were merged for the genome browser view. f A representative locus is shown for the repressed promoter (Gata2)-mediated chromatin interactions during erythroid differentiation. The locations of the annotated Gata2 TSS (+ 1) and candidate enhancers are shown on the bottom