Fig. 1
HA tag ChIP-seq analyses identified unique genomic binding sites of RELAFUS1. a, b Genome-wide RELAFUS1-HA (a) and RELAFUS1−S486E-HA (b) binding demonstrated by HA ChIP-seq analyses in 293T/tv-a cells. Heatmaps represent HA ChIP enrichments at the regions (TSS ± 10 kb) ranked by the sum of the enrichment values. Heatmaps for two biological replicates are shown individually. Input controls are also shown. c, d Bar graphs display the genomic distribution of the RELAFUS1-HA (c) and RELAFUS1−S486E-HA (d) peaks in 293T/tv-a cells. e Volcano plot illustrating differences in gene expression between human RELAFUS positive and all negative ependymomas (DEGs: false discovery rate (FDR) < 0.05, n = 5507). Differences in Log2 fold change in gene expression values are plotted on the x-axis. Adjusted p values calculated using the Benjamin-Hochberg method are plotted on the y-axis. RELAFUS1 target genes annotated within the TSS ± 10 kb are shown as large circles. LMX1B, C11orf95, RELA, CCND1 and L1CAM genes are indicated by the arrows. f Scatter plots showing the mRNA expression of direct RELAFUS1 target genes in the differentially expressed genes (DEGs) (logFC) between human RELAFUS positive and all negative ependymomas. Genes are grouped based on the distance of the RELAFUS1 binding to location to the TSS of the gene (FDR < 0.05, ± 50 kb- ± 1 kb; n = 870, 769, 645, 501, 350, 261, 214 and 179). The expression level of DEGs bound by RELAFUS1 within the TSS ± 10 kb were compared to those bound by RELAFUS1 at other distances as indicated in the x-axis. g, h Venn diagram showing the number of the overlapping between the RELAFUS1 and RELAFUS1−S486E peaks (g) and target genes (h) identified within the TSS ± 10 kb in 293T/tv-a cells. i Scatter plots showing the mRNA expression of target genes differentially bound by RELAFUS1 and/or RELAFUS1−S486E in the DEGs (logFC) between human RELAFUS positive and all negative ependymomas. The target genes of FUS1 (DBPs for RELAFUS1: logFCDBPs > 1, FDR < 0.05, n = 64), S486E (DBPs for RELAFUS1−S486E: logFCDBPs > 1, FDR < 0.05, n = 42) and common (No differential peaks between RELAFUS1 and RELAFUS1−S486E: |logFC|DBPs < 1, n = 404) are shown in the x-axis. DBPs: Differential binding peaks. Statistical differences were assessed with a Mann–Whitney U-test. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001. n.s.: not significant