TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [RNA-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. RNA-seq data in Ctrl and Topors KD AML12 cells.

在哺乳动物细胞核空间中，染色体以层级方式折叠形成由拓扑关联结构域（topologically associating domains, TADs）组成的活性（A）与非活性（B）区室。基因组区域可与核纤层发生互作，此类区域被称为核纤层相关结构域（lamina-associated domains, LADs），其与转录抑制相关。然而，这些三维染色质高级结构背后的分子机制仍未阐明。本研究证实了潜在肿瘤抑制因子——富含精氨酸/丝氨酸的TOP1结合蛋白（TOP1 Binding Arginine/Serine Rich Protein, TOPORS）在基因组组织中的作用。在小鼠肝细胞中敲低Topors基因可促进细胞增殖与迁移，并引发细胞周期S期阻滞。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，其中多数与代谢过程相关。染色质开放性倾向于在基因间区域（包括增强子区域）发生改变。全局水平的染色质-核纤层互作水平下降，LADs的基因组覆盖占比从53.31%降至46.52%。此外，Topors基因敲低会显著增强顺式与反式条件下A、B区室之间的互作强度。与之对应的是，位于A/B区室边界的TAD边界强度出现减弱。综上，本研究数据表明TOPORS可作为染色体折叠的调控因子，为解析肿瘤抑制因子在高级基因组组织结构中的结构塑造作用提供了新的视角。本数据集包含对照组（Ctrl）与Topors敲低（KD）AML12细胞的RNA测序数据。