SETD2-dependent H3K36me3 plays a critical role in epigenetic regulation of the HPV31 life cycle

Abstract

The life cycle of HPV is tied to the differentiation status of its host cell, with productive replication, late gene expression and virion production restricted to the uppermost layers of the stratified epithelium. HPV DNA is histone-associated, exhibiting a chromatin structure similar to that of the host chromosome. Although HPV chromatin is subject to histone post-translational modifications, how the viral life cycle is epigenetically regulated is not well understood. SETD2 is a histone methyltransferase that places the trimethyl mark on H3K36 (H3K36me3), a mark of active transcription. Here, we define a role for SETD2 and H3K36me3 in the viral life cycle. We have found that HPV positive cells exhibit increased levels of SETD2, with SETD2 depletion leading to defects in productive viral replication and splicing of late viral RNAs. Reducing H3K36me3 by overexpression of KDM4A, an H3K36me3 demethylase, or an H3.3K36M transgene also blocks productive viral replication, indicating a significant role for this histone modification in facilitating viral processes. H3K36me3 is enriched on the 3’ end of the early region of the high-risk HPV31 genome in a SETD2-dependent manner, suggesting that SETD2 may regulate the viral life cycle through the recruitment of H3K36me3 readers to viral DNA. Intriguingly, we have found that activation of the ATM DNA damage kinase, which is required for productive viral replication, is necessary for the maintenance of H3K36me3 on viral chromatin and for processing of late viral RNAs. Additionally, we have found that the HPV31 E7 protein maintains the increased SETD2 levels in infected cells through an extension of protein half-life. Collectively, our findings highlight the importance of epigenetic modifications in driving the viral life cycle and identify a novel role for E7 as well as the DNA damage response in the regulation of viral processes through epigenetic modifications.

Epigenetic regulation of human papillomavirus transcription in the productive virus life cycle

“…High-risk E7 mediates the posttranscriptional stabilization of SETD2 resulting in increased levels in HPV31 and HPV16 containing human foreskin keratinocytes. SETD2-dependent H3K36me3 deposition is apparent throughout the viral genome and enriched at the 3′ end of the early gene region in both undifferentiated and differentiated keratinocytes and is essential for both maintenance and productive viral replication [54]. Interestingly, the DNA damage kinase enzyme ataxia-telangiectasia mutated (ATM) is required for maintenance of H3K36Me3 on viral chromatin presumably through inhibition of the demethylases KDM2A and/or KDM4A suggesting that ATM not only facilitates recruitment of DNA damage repair factors to the viral genome but also influences epigenetic status [54].…”

“…SETD2-dependent H3K36me3 deposition is apparent throughout the viral genome and enriched at the 3′ end of the early gene region in both undifferentiated and differentiated keratinocytes and is essential for both maintenance and productive viral replication [54]. Interestingly, the DNA damage kinase enzyme ataxia-telangiectasia mutated (ATM) is required for maintenance of H3K36Me3 on viral chromatin presumably through inhibition of the demethylases KDM2A and/or KDM4A suggesting that ATM not only facilitates recruitment of DNA damage repair factors to the viral genome but also influences epigenetic status [54]. Conversely, HPV E7 has been shown to enhance cellular expression of the H3K27Me3 demethylase KDM6A, resulting in derepression of host genes [55] but the consequences of KDM6A upregulation on the epigenetic status of the viral genome have not been studied.…”

Human Papillomavirus E7 Oncoprotein Subverts Host Innate Immunity via SUV39H1-Mediated Epigenetic Silencing of Immune Sensor Genes

“…In contrast, hrHPV E7 promotes degradation of the retinoblastoma tumor suppressor (pRb) protein, eliciting E2F-mediated transcriptional activation of S-phase genes (2,10). Importantly, both HPV E6 and E7 trigger epigenetic changes in chromatin by altering the expression or the enzymatic activity of a number of epigenetic modifiers, such as histone deacetylases, histone demethylases, histone acetyltransferases, and histone methyltransferases (11)(12)(13)(14)(15)(16)(17)(18)(19). Concomitantly, the oncogenic stimuli triggered by HPV oncoproteins cause host cells to mount an antiviral innate immune response.…”

HPV E7 inhibits cell pyroptosis by promoting TRIM21-mediated degradation and ubiquitination of the IFI16 inflammasome

“…International Publisher MHC-I by deregulating host DNA methylation and histone modification [9][10][11][12]. Moreover, HPV E7 can locate in the cytoplasm to interrupt the cGAS-STING and IFN signaling pathways by interacting with STING, IRF9 or IRF1 [13][14][15].…”