Extended Data Fig. 9: Hi-C mapping reveals that a phase-separation-competent IDR within NUP98–HOXA9 is required to induce formation of CTCF-independent chromatin loops at the leukaemia-related genomic loci.
From: Phase separation drives aberrant chromatin looping and cancer development
a, Matrix of Pearson correlation coefficients of loop counts among and between biological replicates of N-IDRWT/A9 (WT; n = 4 replicates) or N-IDRFS/A9 (FS; n = 4 replicates) conditions. Numbers following WT or FS indicate biological replicate for that condition. b, Example correlation plots of loop counts between biological replicates and conditions. c, All loops were partitioned into either WT- or FS-specific loops and split into separate loop anchors. Loop anchors were then intersected with ChIP–seq peaks of N-IDR/A9 or CTCF. The percentage of observed (Obs.) overlaps for each feature is shown as a vertical blue line. The red line shows the expected (Exp.) distribution of overlaps as determined by randomly sampling loop anchors and calculating the overlap of each feature 1,000 times. P values were determined by summing the number of expected values greater than (or less than if the observed value was less than the mean) the observed value for that feature. d–g, 3C–qPCR assays measuring the change in crosslinking frequency of either an N-IDRWT/A9-specific loop at the PBX3 locus (d, e) or a CTCF-dependent loop (f, g; at Chr17 (41604677–41883642)) after treatment of 293FT stable cells with 10% 1,6-hexanediol for 1 min (+H), relative to mock (+V). The IGV view panels at d and f show the indicated ChIP–seq signals, with positions of the used 3C–PCR primers labelled under IGV tracks. PCR was performed using the same constant forward primer (C) paired with a differently numbered reverse primer (P1 to P4) at each locus tested. Panels e and g are plotted with signals of 3C–qPCR measuring the relative crosslinking frequency at PBX3 (d, e) or a Chr17 locus with CTCF loop (f, g) before (V) and after (H) treatment with 1,6-hexanediol. Signals in e are normalized to those of the N-IDRFS/A9-expressing cells (n = 3 replicated experiments). P values were determined by two-sided t-test. Data are mean ± s.d. of three or six replicates.
