Fig. 4: CRISPRi with a single truncated guide disrupts CTCF binding at multiple loci.
From: Multi-locus CRISPRi targeting with a single truncated guide RNA
a CTCF ChIP of the CTCF bound sites (134) targeted by sg4 in Jurkat cells. Significance with t-test ***P = 5.6 × 10−13. b H3K9me3 ChIP of sg4 targeted perfect match sites (357) with genomic bins plotted (416). Two bins were included in cases where an sg4 site targeted a bin boundary. Significance with t-test ***P = 1.3 × 10−38. Data are aggregated from two independent replicates and presented as median values +/− 1 SD (box), with whiskers extending 1.5x below the first quartile and 1.5x above the third quartile in a and b. c Scatter plot CTCF binding at JASPAR motifs (880k) with 357 perfect match sites (black) and partial match sites (gray). d H3K9me3 density plot for Safe Harbor (S.H., light purple) and sg4 (dark purple) treated Jurkat cells. e Track view of a targeted region depicting CTCF and H3K9me3 signal from 2 replicate experiments (rep). Bars on the bottom depict CTCF perfect match (black) and partial match sites (gray). f dCas9 density plot for Safe Harbor (S.H., light purple) and sg4 (dark purple) treated Jurkat cells. g Volcano plot of CTCF bound sites (400k) with significant 10nt match CTCF sites (black), significant partial match sites (79), and not significant sites. Significance was determined at cutoffs (abs [LFC] > 0.5 and -log10 P > 5) using a linear mixed model and two-sided test that adjusts for multiple hypotheses. h Histogram depicting significant CTCF disrupted sites as a fraction of CTCF bound sites with 0 mismatches (black) up to 4 mismatches (blue). Raw values depicted on each bar. i Logogram of significant perfect match sites (top, 79 sites) and significant partial match sites (bottom, 79 sites) from Jurkat sg4 experiments. Source data are provided as a Source Data file.
