改变的染色质三维结构在人类癌症中影响各种基因组调节因子及后续基因表达。然而，我们对癌症中基因组分层结构的拓扑重排知之甚少。本研究利用原位 Hi-C、RNA-测序和染色质免疫沉淀测序（ChIP-seq）技术，探讨了胆囊癌（GBC）组织和细胞系中染色质区域、拓扑关联域（TADs）和CCCTC 结合因子（CTCF）介导的循环结构的结构重组和功能变化。我们观察到染色质区域 A/B 转换与 CTCF 结合水平和基因表达的改变相关。相对于正常对照，癌症细胞系中存在着增加的 TAD 间互作用与较弱的 TAD 边界。此外，与癌症相比，与染色质重塑和上皮-间质转变激活相关的染色质短环和癌症特异环在癌症中富集。癌症特异的增强子-启动子循环，其包含多个转录因子结合位点，作为调节异常基因表达的中心元素。削减与启动子相连接的每个循环锚定点上的单个增强子导致相应基因表达的抑制。总之，我们的数据提供了癌症基因组分层结构和功能变化的全景图，这些变化推动了 GBC 的发展。© 2023. Higher Education Press.

Altered three-dimensional architecture of chromatin influences various genomic regulators and subsequent gene expression in human cancer. However, knowledge of the topological rearrangement of genomic hierarchical layers in cancer is largely limited. Here, by taking advantage of in situ Hi-C, RNA-sequencing, and chromatin immunoprecipitation sequencing (ChIP-seq), we investigated structural reorganization and functional changes in chromosomal compartments, topologically associated domains (TADs), and CCCTC binding factor (CTCF)-mediated loops in gallbladder cancer (GBC) tissues and cell lines. We observed that the chromosomal compartment A/B switch was correlated with CTCF binding levels and gene expression changes. Increased inter-TAD interactions with weaker TAD boundaries were identified in cancer cell lines relative to normal controls. Furthermore, the chromatin short loops and cancer unique loops associated with chromatin remodeling and epithelial-mesenchymal transition activation were enriched in cancer compared with their control counterparts. Cancer-specific enhancer-promoter loops, which contain multiple transcription factor binding motifs, acted as a central element to regulate aberrant gene expression. Depletion of individual enhancers in each loop anchor that connects with promoters led to the inhibition of their corresponding gene expressions. Collectively, our data offer the landscape of hierarchical layers of cancer genome and functional alterations that contribute to the development of GBC.© 2023. Higher Education Press.