TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [ATAC-seq]

Within mammalian nuclear space, chromosomes are hierarchically folded into active (A) and inactive (B) compartments composed of topologically associating domains (TADs). Genomic regions interact with nuclear lamina, termed lamina-associated domains (LADs), associated with transcriptional repression. However, the molecular mechanisms underlying these 3D chromatin architectures remain undeciphered. Here, we demonstrate the role of a potential tumor suppressor, TOP1 Binding Arginine/Serine Rich Protein (TOPORS), in genome organization. Topors knockdown in mouse hepatocytes results in cell proliferation and migration promotion, as well as arrest in the S phase of the cell cycle. RNA-seq analysis shows that 373 genes are up-regulated, some of which are associated with nuclear structure, and 316 genes exhibit down-regulated, many related to metabolic process. Chromatin accessibility is inclined to alter in the intergenic regions, including enhancers. Chromatin-lamina interactions decrease globally, and the coverage of LADs reduces from 53.31% to 46.52%. Furthermore, Topors knockdown leads to significantly increasing interactions between A and B compartments in cis and in trans. Correspondingly, strength of TAD boundaries located at A/B borders is weakened. Collectively, our data reveal that TOPORS functions as a regulator in chromosome folding, providing novel insights into the architectural role of tumor suppressors in higher-order genome organization. ATAC-seq data in Ctrl and Topors KD AML12 cells.

在哺乳动物细胞核空间中，染色体以层级折叠方式形成由拓扑关联结构域（topologically associating domains, TADs）组成的活跃（A）与非活跃（B）区室。基因组区域与核纤层发生相互作用，此类区域被称为核纤层关联结构域（lamina-associated domains, LADs），与转录抑制过程相关。然而，这些三维染色质高级结构背后的分子机制仍未得到阐明。本研究揭示了一种潜在肿瘤抑制因子——富含精氨酸/丝氨酸的TOP1结合蛋白（TOPORS）在基因组组织中的功能。在小鼠肝细胞中敲低Topors可促进细胞增殖与迁移，并使细胞周期阻滞于S期。RNA测序（RNA-seq）分析显示，共有373个基因表达上调，其中部分基因与细胞核结构相关；另有316个基因表达下调，多数基因与代谢过程相关。染色质可及性在基因间区（包括增强子区域）更易发生改变。全基因组范围内染色质与核纤层的相互作用减弱，核纤层关联结构域的覆盖比例从53.31%降至46.52%。此外，Topors敲低会显著增强A、B区室之间的顺式与反式相互作用。相应地，位于A/B区室边界的拓扑关联结构域边界强度也被削弱。综上，本研究数据表明TOPORS作为染色体折叠的调控因子，为阐明肿瘤抑制因子在高阶基因组组织中的结构功能提供了全新视角。本数据集包含对照组与Topors敲低的AML12细胞的ATAC测序（ATAC-seq）数据。