Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functionalMYCsuperenhancers 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, includingMYCproto-oncogene, were under the control of superenhancers whose activities were globally repressed upon viral reactivation. The eRNA-expressingMYCsuperenhancers were located downstream of theMYCgene in KSHV-infected PELs and played a key role inMYCexpression. RNAi-mediated depletion or dCas9-KRAB CRISPR inhibition ofeRNAexpression significantly reducedMYCmRNA level in PELs, as did the treatment of an epigenomic drug that globally blocks superenhancer function. Finally, while cellular IRF4 acted uponeRNAexpression and superenhancer function forMYCexpression during latency, KSHV viral IRF4 repressed cellularIRF4expression, decreasingMYCexpression 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.