ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [Cell_lines_ChIP, FUUR1, FUUR1_VCP]

ChIPseq experiments identify that ASPSCR1-TFE3 defines active enhancers across the genome and co-distributes with VCP/p97. RNAseq after knock-down of ASPSCR1-TFE3 or VCP, inhibition of VCP, or overexpression of each in alveolar soft part sarcoma cell lines demonstrates their co-dependence. HiChIP defines chromatin conformations that surround ASPSCR1-TFE3 targets and are lost on VCP knock-down. ASPS cell lines, tumors from ASPS mouse model and tumors from ASPS patients are used for ChIP-seq with antibodies against ASPSCR1, VCP, POLII and various histone modifications. RNAseq in ASPS cell lines after application of siRNA against control, ASPSCR1-TFE3, or VCP, or application of VCP inhibitor CB-5083. H3K27ac-HiChIP in the FU-UR-1 cell line at baseline and after 6 days of siRNA against VCP.

染色质免疫共沉淀测序（ChIP-seq）实验证实，ASPSCR1-TFE3可在全基因组范围内界定活性增强子，并与VCP/p97共分布。在腺泡状软组织肉瘤（alveolar soft part sarcoma, ASPS）细胞系中，通过敲低ASPSCR1-TFE3或VCP、抑制VCP活性，或是过表达二者后开展的RNA测序（RNA-seq）实验，证实了二者的共依赖性。HiChIP实验明确了ASPSCR1-TFE3靶位点周边的染色质构象，该构象会在VCP敲低后消失。本数据集使用ASPS细胞系、ASPS小鼠模型的肿瘤组织以及ASPS患者的肿瘤样本，搭配针对ASPSCR1、VCP、RNA聚合酶II（POLII）及多种组蛋白修饰的抗体进行染色质免疫共沉淀测序（ChIP-seq）。在ASPS细胞系中，分别施加针对阴性对照、ASPSCR1-TFE3或VCP的小干扰RNA（siRNA）处理，或是施加VCP抑制剂CB-5083后，开展RNA测序（RNA-seq）。在FU-UR-1细胞系中，于基线状态以及针对VCP的siRNA处理6天后，开展H3K27ac标记的HiChIP实验。