Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs

Abstract

Enhancers play indispensable roles in cell proliferation and survival through spatiotemporally regulating gene transcription. Active enhancers and superenhancers often produce noncoding enhancer RNAs (eRNAs) that precisely control RNA polymerase II activity. Kaposi’s sarcoma-associated herpesvirus (KSHV) is a human oncogenic gamma-2 herpesvirus that causes Kaposi’s sarcoma and primary effusion lymphoma (PEL). It is well characterized that KSHV utilizes host epigenetic machineries to control the switch between two lifecycles, latency and lytic replication. However, how KSHV impacts host epigenome at different stages of viral lifecycle is not well understood. Using global run-on sequencing (GRO-seq) and chromatin-immunoprecipitation sequencing (ChIP-seq), we profiled the dynamics of host transcriptional regulatory elements during latency and lytic replication of KSHV-infected PEL cells. This revealed that a number of critical host genes for KSHV latency, including MYC proto-oncogene, were under the control of superenhancers whose activities were globally repressed upon viral reactivation. The eRNA-expressing MYC superenhancers were located downstream of the MYC gene in KSHV-infected PELs and played a key role in MYC expression. RNAi-mediated depletion or dCas9-KRAB CRISPR inhibition of eRNA expression significantly reduced MYC mRNA level in PELs, as did the treatment of an epigenomic drug that globally blocks superenhancer function. Finally, while cellular IRF4 acted upon eRNA expression and superenhancer function for MYC expression during latency, KSHV viral IRF4 repressed cellular IRF4 expression, decreasing MYC expression and thereby, facilitating lytic replication. These results indicate that KSHV acts as an epigenomic driver that modifies host epigenomic status upon reactivation by effectively regulating host enhancer function.

Primary effusion lymphoma enhancer connectome links super-enhancers to dependency factors

“…We identified >8000 enhancer–promoter, enhancer–enhancer, and promoter–promoter interactions in these cell lines. The connectome linked SEs to dependency factors MYC, IRF4, MCL, MDM2, and CCND2 66 .…”

GWAS associated Variants, Non-genetic Factors, and Transient Transcriptome in Multiple Sclerosis Etiopathogenesis: a Colocalization Analysis

“…As a matter of fact, the sequence variability of these regions and the strict time-dependence of their transcription could be instrumental to adaptive features; however, these same features make these regions susceptible to become dysfunctional or to be the targets of pathogenic interaction. In some instances, these detrimental interactions come from outside the cell, such as in the case of EBV interference with host transcription (Mechelli R., 2021, Accepted; Park et al, 2020), and the pathogenic consequences of vitamin D deficiency; in other cases, the dysfunction develops within the cell, such as the tumorigenic activity of AID in B cells (Meng et al, 2014; Qian et al, 2014).…”

Polyamine biosynthesis and eIF5A hypusination are modulated by the DNA tumor virus KSHV and promote KSHV viral infection

“…Indeed, we found that ODC1 is slightly upregulated in iSLK.BAC16 vs SLK cells (Fig 1F). In contrast, KSHV lytic induction resulted in the decrease of ODC1 protein in Dox-treated iSLK.BAC16 (Fig 1G), likely because c-Myc is silenced due to KSHV lytic reactivation [47,48]. Consistently, we also observed that ODC1 mRNA level also decreased at 3 dpi in primary tonsillar B cells isolated from healthy donors, known to be susceptible to KSHV infection and maintain active lytic replication [49], which were spinoculated with KSHV.BAC16 viruses, followed by RT-qPCR analysis (Fig 1H).…”