Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors.
Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors.
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潜伏的HIV感染的表观基因组学特征确定了潜伏期调节转录因子。
DOI：
10.1371/journal.ppat.1009346
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发表时间：
2021-03
期刊：
影响因子：
6.7
通讯作者：
Browne EP
中科院分区：
文献类型：
--
作者：
Jefferys SR;Burgos SD;Peterson JJ;Selitsky SR;Turner AW;James LI;Tsai YH;Coffey AR;Margolis DM;Parker J;Browne EP
HIV在CD4T细胞中的转录沉默产生了一个潜伏感染细胞的储存库，这些细胞可以在治疗中断后重新传播感染。因此，这些细胞是治愈艾滋病毒感染的主要障碍，但人们对它们的特征知之甚少。为了进一步理解潜伏期的分子机制，我们描述了一个HIV潜伏期的原始细胞模型，在该模型中，感染细胞采用了不同的转录命运。在这个模型中，我们观察到潜伏期是一种稳定的、可遗传的状态，通过细胞分裂传递。利用转座子可及染色质测序分析(ATACseq)，我们发现潜伏感染的细胞表现出极大的前病毒可及性，这表明病毒基因表达存在基于染色质的结构性障碍。通过对宿主细胞转录因子活性的定量，我们观察到在潜伏感染的细胞中，Forkhead和Kruppel样因子转录因子(TF)的活性升高，而AP-1、RUNX和GATA转录因子的活性降低。有趣的是，具有不同作用机制的潜伏期反转剂导致前病毒染色质重新打开的不同模式。我们观察到染色质绝缘体CTCF的结合位点在感染的CD4T细胞差异开放的染色质中高度丰富。此外，CTCF的耗尽抑制了艾滋病毒的潜伏期，确认这一因素在潜伏期的启动或执行中发挥了关键作用。这些数据表明，HIV潜伏在具有独特的TF活性模式的细胞中优先发展，这种模式促进封闭的前病毒结构并抑制病毒基因的表达。此外，这些发现确认CTCF是HIV潜伏期的一个新的调节因子。在抗病毒治疗期间，艾滋病毒能够通过进入病毒潜伏状态而持续存在，在这种状态下，病毒基因的表达大大减少。如果治疗中断，这些潜伏感染的细胞可能会重新传播感染，因此是治愈艾滋病毒的主要障碍。确定导致这种状态的机制将有助于确定阻断或消除艾滋病毒潜伏期的战略，从而治愈感染。通过观察感染的CD4T细胞中HIV基因的表达，我们分离出HIV进入潜伏期的细胞，并确定了它们与病毒复制活跃的细胞的区别特征。我们发现，潜伏感染的细胞具有高活性的特定转录因子，包括叉头因子和Kruppel样因子。我们还发现CTCF，一种负责调节基因组结构域相互隔离的蛋白质，是建立HIV潜伏期所必需的。开发针对这些因素的药物可能会导致消除艾滋病毒携带者的新战略。
Transcriptional silencing of HIV in CD4 T cells generates a reservoir of latently infected cells that can reseed infection after interruption of therapy. As such, these cells represent the principal barrier to curing HIV infection, but little is known about their characteristics. To further our understanding of the molecular mechanisms of latency, we characterized a primary cell model of HIV latency in which infected cells adopt heterogeneous transcriptional fates. In this model, we observed that latency is a stable, heritable state that is transmitted through cell division. Using Assay of Transposon-Accessible Chromatin sequencing (ATACseq) we found that latently infected cells exhibit greatly reduced proviral accessibility, indicating the presence of chromatin-based structural barriers to viral gene expression. By quantifying the activity of host cell transcription factors, we observe elevated activity of Forkhead and Kruppel-like factor transcription factors (TFs), and reduced activity of AP-1, RUNX and GATA TFs in latently infected cells. Interestingly, latency reversing agents with different mechanisms of action caused distinct patterns of chromatin reopening across the provirus. We observe that binding sites for the chromatin insulator CTCF are highly enriched in the differentially open chromatin of infected CD4 T cells. Furthermore, depletion of CTCF inhibited HIV latency, identifying this factor as playing a key role in the initiation or enforcement of latency. These data indicate that HIV latency develops preferentially in cells with a distinct pattern of TF activity that promotes a closed proviral structure and inhibits viral gene expression. Furthermore, these findings identify CTCF as a novel regulator of HIV latency. HIV is able to persist during antiviral therapy by entering a state of viral latency, in which viral gene expression is greatly reduced. These latently infected cells can re-seed infection if therapy is interrupted, and thus represent a major obstacle to an HIV cure. Identifying the mechanisms that lead to this state will help to identify strategies to block or eliminate HIV latency, leading to a cure for infection. By observing HIV gene expression in infected CD4 T cells, we isolated cells in which HIV has entered latency and identified characteristics that distinguish them from cells with active viral replication. We found that latently infected cells have elevated activity of specific transcription factors including Forkhead TFs and Kruppel-like factors. We also identify CTCF, a protein responsible for mediating insulation of genome domains from each other, as being required for the establishment of HIV latency. Developing agents to target these factors may lead to new strategies to eliminate the HIV reservoir.
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DOI：
10.1073/pnas.94.24.13193
发表时间：
1997-11-25
影响因子：
11.1
作者：
Chun, TW;Stuyver, L;Fauci, AS
通讯作者：
Fauci, AS
影响因子：
6.4
作者：
Crooks, Amanda M.;Bateson, Rosalie;Archin, Nancie M.
通讯作者：
Archin, Nancie M.
影响因子：
5.4
作者：
Friedman, Julia;Cho, Won-Kyung;Karn, Jonathan
通讯作者：
Karn, Jonathan
影响因子：
3.7
作者：
Boeva V
通讯作者：
Boeva V
影响因子：
64.5
作者：
Ho YC;Shan L;Hosmane NN;Wang J;Laskey SB;Rosenbloom DI;Lai J;Blankson JN;Siliciano JD;Siliciano RF
通讯作者：
Siliciano RF