Fig. 3. VCP co-localizes on chromatin to target loci of AT3.

a Heatmaps of overlapping enrichment in ChIP-seq with antibodies against AT3 and VCP in human FU-UR-1 cells, ASPS-1 cells, two human ASPS tumors, and 3 mouse ASPS tumors. Each heatmap is centered on peaks across the genome, sorted by AT3 enrichment, representing at least 2 replicates. b Example tracks with overlaid ChIP-seq enrichments of AT3 and VCP at selected highly enriched target genes (See also Supplementary Fig. 4a). Tracks scaled together 0 to 15 reads per million (RPM). c Graph depicting mean ± standard deviation as well as raw value points of fold-enrichment of double cross-linked VCP ChIP over input chromatin by quantitative polymerase chain reaction (qPCR) for two AT3-expressing cell lines (ASPS-1 and FU-UR-1) and two control cell lines (HCT116, colon cancer; ASKA, synovial sarcoma) at a panel of selected target genes and one negative control locus (CCND2). Two-tailed Student’s t-test generated p-values as indicated. d Similar graph of VCP ChIP enrichment over input for FU-UR-1 cells exposed for 48 h to control siSCR or one of two siTFE3s directed against AT3. e Similar graph of VCP ChIP enrichment over input for HEK293T cells transfected with GFP control, TFE3 control, ASPSCR1 control, AT3.1 or AT3.2.