Fig. 2

Disproportionate occupancy of FUS-DDIT3 across myxoid LPS (MLPS) genome. a Effect of FUS-DDIT3 silencing on cell viability of MLS402 cells. Data are presented as mean ± SEM; n = 3. Two-tailed Student’s t-test was used. b Pie chart showing the genomic occupancy of FUS-DDIT3 peaks in MLS402 cells. Top de novo DNA-binding motif of FUS-DDIT3 was identified by Homer (hypergeometric test). TSS, transcription start site; UTR, untranslated region; TTS, transcription termination site. c Heatmaps for the ChIP-seq signals of indicated antibodies ± 2 kb from TSS in MLS402 cells. d Differential enrichment of FUS-DDIT3 in SE and typical enhancer (TE) regions. e Rank order of stitched FUS-DDIT3 ChIP-seq signals in MLS402 cells. Representative FUS-DDIT3-overloaded genes and their rankings were highlighted. f Venn-diagram showing number of genes with their SEs overloaded with H3K27ac and/or FUS-DDIT3 in MLS402 cells. g, h FUS-DDIT3/H3K27ac double-positive SEs were associated with high basal gene expression in g MLS402 and h primary MLPS samples (n = 20). Wilcoxon signed-rank test was applied. FPKM, fragments per kilobase million. Box plots indicate median value (center line), first and third quartiles (box limits), as well as minimum and maximum values (whiskers) after excluding outliers (dots). i Co-immunoprecipitation (IP) between endogenous BRD4 and FUS-DDIT3 in MLS402 cells. j GFP-IP showing the interaction between FUS-DDIT3 and BET proteins. FUS-DDIT3 was co-expressed with either EGFP or EGFP-tagged BET proteins in HEK293T cells. k Co-localization of FUS-DDIT3 and BRD4 across the genome of MLS402 cells. Heatmaps were used to present the ChIP-seq signals of indicated antibodies ± 2.5 kb from the peak centers of FUS-DDIT3 in MLS402 cells. l Quantitative reverse transcription PCR (qRT-PCR) analysis showing the mRNA levels of FST, IL8, BCAT1, and SMURF2 upon small-interfering RNA (siRNA)-mediated knockdown of FUS-DDIT3, BRD2, BRD3, and BRD4, relative to si-NT. RNA was harvested 48 h post transfection in MLS402 cells. Data are presented as mean ± SEM; n = 3. Significance was reported within each target gene based on one-way analysis of variance (ANOVA). n.s., not significant; *p < 0.05; **p < 0.01; ***p < 0.001. Source data are provided as a Source Data file