Single-genome analysis reveals heterogeneous association of the Herpes Simplex Virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts
Single-genome analysis reveals heterogeneous association of the Herpes Simplex Virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts
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单基因组分析揭示了感染人成纤维细胞后单纯疱疹病毒基因组与 H3K27me2 和阅读器 PHF20L1 的异质关联
DOI：
10.1101/2023.12.03.569766
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Francois A
中科院分区：
文献类型：
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作者：
Francois A
疱疹病毒基因组进入不同细胞类型后的命运被认为调节感染的结果。对于单纯疱疹病毒1（HSV-1），神经元的潜伏感染的特征在于与组蛋白H3（H3 K27 me）上标记有Polycomb沉默相关的赖氨酸27甲基化的抑制性异染色质相关。然而，H3 K27甲基化是否在抑制非神经元细胞中的裂解基因表达中起作用尚不清楚。为了解决这一知识缺口，并考虑到病毒基因组的命运和HSV-1感染的结果可能是异质性的，我们开发了一种测定法来量化感染成纤维细胞的单个病毒基因组病灶内组蛋白修饰的丰度。使用这种方法，结合大量表观遗传学技术，我们无法检测H3 K27 me 3在成纤维细胞的HSV-1裂解感染期间的任何作用。相比之下，我们可以检测到较少研究的H3 K27 me 2病毒基因组的亚群，这是一致的作用，促进裂解基因表达的H3 K27脱甲基酶。此外，病毒基因组与H3 K27 me 2阅读蛋白PHF 20 L1共定位，并且这种关联通过抑制H3 K27脱甲基酶UTX和JMJD 3而增强。值得注意的是，在不存在早幼粒细胞白血病核体的情况下，用转录缺陷型病毒感染后，H3 K27 me 2对病毒基因组的靶向增强。总的来说，这些研究暗示了H3 K27 me 2在成纤维细胞相关HSV基因组沉默中的作用，其方式依赖于基因组亚核定位和转录活性。重要性研究DNA病毒在不同细胞类型中基因沉默的潜在机制对于理解感染的不同结果是重要的，特别是对于像疱疹病毒这样的病毒，它们可以在不同的细胞类型中经历不同类型的感染。此外，研究染色质与病毒基因组的关联有助于了解DNA过程的表观遗传调控机制。然而，越来越多的人认识到单细胞甚至单病毒基因组水平上感染结果的异质性。在这里，我们描述了一种新的检测方法，用于定量病毒基因组病灶与染色质蛋白，并显示，基因组的一部分被靶向沉默H3 K27 me 2和相关的阅读器蛋白PHF 20 L1。这项研究提出了关于H3 K27 me 2特异性靶向病毒基因组的机制、表观遗传异质性对疱疹病毒感染的贡献以及PHF 20 L1在调节DNA病毒感染结果中的作用的重要问题。
The fate of herpesvirus genomes following entry into different cell types is thought to regulate the outcome of infection. For the Herpes simplex virus 1 (HSV-1), latent infection of neurons is characterized by association with repressive heterochromatin marked with Polycomb silencing-associated lysine 27 methylation on histone H3 (H3K27me). However, whether H3K27 methylation plays a role in repressing lytic gene expression in non-neuronal cells is unclear. To address this gap in knowledge, and with consideration that the fate of the viral genome and outcome of HSV-1 infection could be heterogeneous, we developed an assay to quantify the abundance of histone modifications within single viral genome foci of infected fibroblasts. Using this approach, combined with bulk epigenetic techniques, we were unable to detect any role for H3K27me3 during HSV-1 lytic infection of fibroblasts. By contrast, we could detect the lesser studied H3K27me2 on a subpopulation of viral genomes, which was consistent with a role for H3K27 demethylases in promoting lytic gene expression. In addition, viral genomes co-localized with the H3K27me2 reader protein PHF20L1, and this association was enhanced by inhibition of the H3K27 demethylases UTX and JMJD3. Notably, targeting of H3K27me2 to viral genomes was enhanced following infection with a transcriptionally defective virus in the absence of Promyelocytic leukemia nuclear bodies. Collectively, these studies implicate a role for H3K27me2 in fibroblast-associated HSV genome silencing in a manner dependent on genome sub-nuclear localization and transcriptional activity.IMPORTANCEInvestigating the potential mechanisms of gene silencing for DNA viruses in different cell types is important to understand the differential outcomes of infection, particularly for viruses like herpesviruses that can undergo distinct types of infection in different cell types. In addition, investigating chromatin association with viral genomes informs on the mechanisms of epigenetic regulation of DNA processes. However, there is a growing appreciation for heterogeneity in the outcome of infection at the single cell, and even single viral genome, level. Here we describe a novel assay for quantifying viral genome foci with chromatin proteins and show that a portion of genomes are targeted for silencing by H3K27me2 and associate with the reader protein PHF20L1. This study raises important questions regarding the mechanism of H3K27me2-specific targeting to viral genomes, the contribution of epigenetic heterogeneity to herpesvirus infection, and the role of PHF20L1 in regulating the outcome of DNA virus infection.