Extended Data Fig. 10: Integrated genomic analysis for example genes.

a. Normalized RNA-seq reads of indicated genes that are shown for integrated genomic analysis, in Vector (V), WT (W), ΔcIDR (c), UTX-eIF_IDR (e), ΔcTPR (T) samples. One repeat of the Vector sample was set to 1. HK2 gene (boxed) differs from the other genes in that it was repressed by UTX WT but not ΔcIDR. b. Integrated genomic analysis for MX2-MX1 cluster, OAS1-3-2 cluster, OASL, UBE2W-LY96 cluster, KCNJ2, and HK2. as examples for UTX condensates-regulated gene expression associated with chromatin interactions. Top, PRO-seq 3′ end coverage tracks (red, + strand; blue, – strand), with the same scale for all samples. A higher MX2 transcriptional activity in WT than ΔcIDR cells is shown by the denser WT PRO-seq signals when IGV-zoomed in in the dashed box on top. Also note the higher transcriptional activity of LY96 in UTX WT than vector and ΔcIDR cells, as shown by the PRO-seq signal density and the - strand eRNA (in green oval) at both LY96 promoter and gene-downstream enhancer. Green arrows show the higher H3K4me1 or H3K27ac signal in WT than the other two cell samples at OASL promoter. PRO-seq confirmed transcriptional changes and, together with the H3K4me1 and H3K27ac peaks, revealed actively and bi-directionally transcribing enhancers. Note that H3K27ac and/or H3K4me1 were increased at MX2, OASL, and KCNJ2 promoters or enhancers upon WT but not ΔcIDR expression. Bottom, H3K27ac HiChIP arc plots of loops are shown on WashU EpiGenome Browser. All arc plots have the same scale for statistical significance (arc darkness) of the loop calls. Black arrows indicate normal loops in WT-expressing cells that were lost in vector, ΔcIDR, or ΔTPR cells. Cyan arrows indicate loops normally suppressed by UTX WT but aberrantly formed in vector, ΔcIDR, or ΔTPR cells.