基于原位Hi-C技术对人肝细胞癌细胞系PLC/PRF/5和正常人肝细胞系L02的三维基因组对比测序分析

3D organization profiling of human hepatocellular carcinoma cell line PLC/PRF/5 in comparison with normal human liver cell line L02 by in situ Hi-C

摘要:

肝细胞癌 (Hepatocellular carcinoma，HCC) 的肿瘤发生是基因组突变和表观遗传修饰变化积累的结果，但是HCC发生过程中的三维基因组构造变化仍然缺乏研究。基于此，在人源HCC细胞系PLC/PRF/5和人源正常肝细胞系L02中进行了原位Hi-C分析，并辅以转录组测序以及SMC3/CTCF/H3K27ac的染色质免疫共沉淀测序分析，借此比较两细胞系的三维基因组差异。结果显示，相较于正常肝细胞系，在PLC/PRF/5中发生了显著的染色体结构区域 (Compartment) 转换、三维拓扑结构域 (Topologically associating domains，TAD) 滑动和染色质环(Loop) 的变化。以上这些染色质空间结构的差异与HCC细胞系中肿瘤特异性基因表达和启动子开放性增高具有相关性。因此，在PLC/PRF/5细胞系中的染色质三维结构差异可能在HCC肿瘤发生的表观遗传学机制中具有重要作用。

关键词:肝细胞癌，三维基因组，原位Hi-C，染色质拓扑结构域，染色质环

Abstract:

Genetic and epigenetic alterations accumulate in the process of hepatocellular carcinogenesis, but the role of genomic spatial organization in HCC is still unknown. Here, we performed in situ Hi-C in HCC cell line PLC/PRF/5 compared with normal liver cell line L02, together with RNA-seq and ChIP-seq of SMC3/CTCF/H3K27ac. The results indicate that there were significant compartment switching, TAD shifting and loop pattern altering in PLC/PRF/5. These spatial changes are correlated with abnormal gene expression and more opening promoter regions of the HCC cell line. Thus, the 3D genome organization alterations in PLC/PRF/5 are important in epigenetic mechanisms of HCC tumorigenesis.

Key words:hepatocellular carcinoma, 3D genome, in situ Hi-C profiling, chromatin TAD, chromatin loop