A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth

Abstract

Epstein-Barr virus (EBV) immortalization of resting B lymphocytes (RBLs) to lymphoblastoid cell lines (LCLs) models human DNA tumor virus oncogenesis. RBL and LCL chromatin interaction maps are compared to identify the spatial and temporal genome architectural changes during EBV B cell transformation. EBV induces global genome reorganization where contact domains frequently merge or subdivide during transformation. Repressed B compartments in RBLs frequently switch to active A compartments in LCLs. LCLs gain 40% new contact domain boundaries. Newly gained LCL boundaries have strong CTCF binding at their borders while in RBLs, the same sites have much less CTCF binding. Some LCL CTCF sites also have EBV nuclear antigen (EBNA) leader protein EBNALP binding. LCLs have more local interactions than RBLs at LCL dependency factors and super-enhancer targets. RNA Pol II HiChIP and FISH of RBL and LCL further validate the Hi-C results. EBNA3A inactivation globally alters LCL genome interactions. EBNA3A inactivation reduces CTCF and RAD21 DNA binding. EBNA3C inactivation rewires the looping at the CDKN2A/B and AICDA loci. Disruption of a CTCF site at AICDA locus increases AICDA expression. These data suggest that EBV controls lymphocyte growth by globally reorganizing host genome architecture to facilitate the expression of key oncogenes.

Epstein‐Barr virus and host cell 3D genome organization

“…81 In addition, our recent study examining the genome-wide effect of EBNA3A on genome organization using HiChIP find that the inactivation of EBNA3A also increases the long-range DNA and DNA interactions between MTAP and CDKN2A/2B loci. 108 These data suggest that similar to BCL2L11, EBNA3A and EBNA3C may suppress p14 ARF and p16 INK4A expression by preventing the formation of local transcription regulation hubs between MTAP and CDKN2A/2B.…”

“…Approximately 30% of genes essential for LCL growth are linked to EBV enhancers 81 . To determine the effect of EBV infection on 3D genome organization changes of human B cell in both space and time, Chong et al compared the Hi‐C maps in RBLs and LCLs generated from the same B lymphocytes 108 . EBV infection induces global genome reorganization.…”

Viral remodeling of the 4D nucleome

“…For this strategy, methods such as circular chromosome conformation capture (4C) and Capture Hi–C (CHi–C) are valuable because they magnify or enrich specific associations linked to viral genomes 13 – 15 . Additionally, techniques such as ChIA-PET and HiChIP can be employed to identify genomic associations mediated by viral or cellular proteins 16 – 18 . The application of 3D genomic methodologies has significantly impacted various aspects of virology, which can be categorized into three main interactions: viral–viral associations, viral–host associations, and host–host associations modulated by viral infection.…”

“…Indeed, these methods have been instrumental in delineating the tethering sites of viral episomes to host chromosomes 20 , 22 – 24 . While 4C and CHi–C increase the resolution of associations with EBV episomes, Hi-C offers an understanding of these attachment sites within the context of the 3D structure of the host genome 18 , 22 , 23 , 25 . These tethering sites of viral episomes have been characterized in EBV, KSHV, and HBV, accounting for different cell types and latency patterns 4 .…”

“…Host‒host 3D genome interactions that change upon viral infection have been characterized for various virus infections and latency types. Remodeling of the host 3D genome was mapped by HiChIP and Hi–C for EBV-infected cells, and changes associated with B-cell immortalization, latency type, or disease status were compared 18 , 21 , 27 – 29 . Host 3D genome structures have also been characterized at the tethering sites of several episomal tumor viruses, including EBV, KSHV, and HBV, revealing cell type- and virus-specific variations 20 , 25 , 30 , 31 .…”