Extended Data Fig. 6: The phase-separation-promoting property within F-IDR is sufficient to induce the enhanced binding of the chimeric transcription factor.
From: Phase separation drives aberrant chromatin looping and cancer development
a, Heat maps showing the k-mean clustering of ChIP–seq signals for chimeric transcription factors that contain the NUP98 IDR (N-IDRWT/A9 and N-IDRFS/A9, two panels on the left) or FUS IDR (F-IDRWT/A9 and F-IDRYS/A9, two panels on the right) reveal a similarly enhanced binding for the LLPS-competent chimera that carries a wild-type form of IDR, relative to its LLPS-incompetent IDR mutant, in 293FT stable expression cells. Note that, although to a lesser degree, the artificially created F-IDRWT/A9 fusion also displays a broad, super-enhancer-like binding pattern at the same sites observed with the N-IDRWT/A9 fusion. b, Pie chart showing percentage distribution of the indicated genomic annotation feature among the ChIP–seq peaks of GFP-tagged F-IDRWT/A9 (left) or F-IDRYS/A9 (right) in the 293FT stable expression cells. c, Heat maps (left) and its averaged ChIP–seq signal distribution profiles (right) for k-mean clustered peaks of N-IDRWT/A9 in the transformed mouse HPSCs. d, Venn diagram showing overlap between the annotated genes associated with the clusters 1–3 of N-IDRWT/A9 ChIP–seq peaks detected in the transformed mouse HPSCs (left) and the 293FT stable expression cells (right). Examples of the shared oncogenes are shown below. e, IGV views of N-IDRWT/A9 ChIP–seq signals (GFP-tagged) at the indicated loci in mouse HSPCs transformed by this chimera. f, ChIP–qPCR to assess the binding of GFP-tagged N-IDRWT/A9 or N-IDRFS/A9 at CCL15 (a negative control region), PBX3 and HOXA9 in the 293FT stable cells after treatment with 10% 1,6-hexanediol for 1 min (+H), relative to mock (+V). ChIP signals, normalized to those of input, are presented as mean ± s.d. of three replicate experiments. g, ChIP–qPCR to assess the binding of GFP-tagged F-IDRWT/A9 or F-IDRYS/A9 at CCL15 (a negative control region), PBX3 and HOXA9 in the 293FT stable cells. ChIP signals, normalized to those of input, are presented as mean ± s.d. of three replicates.
