Cajal Bodies Reorganizes The 3D Genome By Shaping The Histone Genes In Hepatocellular Carcinoma

The mechanisms underlying the formation of biomolecular condensates(BMCs)in cancer progression and the role that they play in the spatiotemporal reorganization of the genome remain poorly understood.Here we explore the potential role of the Cajal bodies(CBs)in the genome organization and gene expression of liver carcinogenesis with a poor prognosis.We initially observed that Coilin,a self-interacting scaffold protein essential for CBs formation,was significantly up-regulated in liver cancer cells and tissues.Furthermore,we observed that knocking out Coilin in liver cancer Hep G2 cells reduced their proliferation and promoted apoptosis.Objective: To explore the expression of Cajal Bodies in liver cancer;to explore whether Cajal Bodies regulate the growth of liver cancer cells;To explore how Cajal Bodies regulate the growth of liver cancer cells;To screen genes that interact with Cajal Bodies.Research significance: The evaluation of the complex three-dimensional genomic structure reconstruction of Cajal bodies in the process of liver cancer has revealed the important functions of Cajal bodies in regulating specific genomic regions,thereby promoting the development of cancer.Methods: RNA-seq,CRISPR/Cas9,High-through chromosome conformation capture(Hi-C).Results: Using RNA-seq in a comparative analysis of differential gene expression in wild-type and Coilin knockout Hep G2 cells,a close functional link between CBs and the expression of replication-dependent histone genes was revealed.Positional gene enrichment analysis showed that upon Coilin knockout,gene expression of the major histone gene cluster(HIST1)present on chromosome 6 was the most significantly downregulated.High-through chromosome conformation capture(Hi-C)mapping further demonstrated that the HIST1 gene cluster was located at the boundary of topologically associated domain(TAD)and that chromatin loops across the HIST1 gene cluster were reduced after Coilin knockout.Additionally,Coilin knockout led to the subdivision of the TAD containing the RNU1 gene cluster(one of the most frequent CBs nucleation sites)present in control cells into two smaller sub-TAD.Additionally,chromatin loops across RNU1 gene cluster were decreased in Coilin knockout cells.Importantly,expression of HIST1 genes was also elevated in liver cancer tissues as compared to normal liver tissues.Conclusions: Overall,the results indicate that CBs formation in highly proliferating liver cancer cells is correlated with changes in the 3D-spatial genome structure increasing expression of histone and spliceosomal gene clusters.