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.
- Author:
Haolin HU
1
;
Xiaoqiang CHAI
1
;
Liyong WANG
1
;
Jiabin CAI
1
;
Fei LAN
1
Author Information
- Publication Type:Journal Article
- Keywords: 3D genome; chromatin TAD; chromatin loop; hepatocellular carcinoma; in situ Hi-C profiling
- MeSH: Carcinoma, Hepatocellular/genetics*; Cell Line; Cell Line, Tumor; Genomics; Humans; Liver Neoplasms/genetics*
- From: Chinese Journal of Biotechnology 2021;37(1):331-341
- CountryChina
- Language:Chinese
- 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.
