Tat controls RNA Polymerase II and the epigenetic landscape to precisely rewire cellular transcriptional programs (RNA-Seq)

Transcription factors mediate precise regulation of gene expression programs to modulate key biological processes. In addition to controlling HIV transcription, Tat appears to modulate cellular transcription to alter the biology of target immune cells and generate a permissive state for HIV infection. However, the molecular mechanisms of transcriptional control have remained elusive. Here, we identified the direct target genes of Tat using genomics and defined mechanisms by which Tat selectively rewires cellular transcriptional programs. Interestingly, Tat functions as both transcriptional activator and repressor of a defined set of genes sharing functional annotations and regulated by master transcriptional regulators such as T-cell identity factors. Tat is recruited to precise genomic domains (promoters and intragenic enhancers) through interaction with master transcriptional regulators to control both the transcription initiation and elongation steps. Tat mediates transcription initiation by modulating Pol II recruitment to promoters and intragenic enhancers and fine-tuning chromatin looping. Tat stimulates or blocks RNA Polymerase (Pol) II recruitment or promoter-proximal pause release thereby promoting gene activation or repression, respectively. Global analysis of chromatin signatures revealed correlation of transcription activity marks with Pol II recruitment or pause release status at gene promoters and enhancers, and transcription elongation at coding units. We propose that Tat has evolved these unique properties to hijack precise genomic domains to control cellular transcription using unexpected regulatory mechanisms, which showed marked differences to the regulation of the HIV genome. Our studies also reveal that Tat can be used as a molecular probe to decode general principles of transcriptional regulation. Overall design: Tat vs. GFP

转录因子（Transcription factors）介导对基因表达程序的精准调控，进而调控关键生物学过程。除调控人类免疫缺陷病毒（HIV）的转录外，Tat反式激活蛋白（Tat）似乎还可调控细胞转录，以改变靶免疫细胞的生物学特性，并为HIV感染营造许可状态。然而，此类转录调控的分子机制迄今仍不明确。本研究通过基因组学手段鉴定了Tat的直接靶基因，并阐明了Tat选择性重塑细胞转录程序的分子机制。值得注意的是，Tat可作为特定基因集的转录激活因子与抑制因子发挥双重功能：这类基因共享功能注释，且受T细胞身份因子等核心转录调控因子的调控。Tat通过与核心转录调控因子相互作用，被招募至精准的基因组区域（启动子与基因内增强子），从而同时控制转录起始与延伸两个步骤。Tat通过调控RNA聚合酶（RNA Polymerase, Pol II）在启动子与基因内增强子处的招募，并微调染色质环化，以此介导转录起始过程。Tat可促进或阻断RNA聚合酶II的招募或启动子近端暂停释放，从而分别介导基因的激活或抑制。对染色质特征的全局分析显示，转录活性标记与基因启动子和增强子处的Pol II招募或暂停释放状态，以及编码区的转录延伸存在显著相关性。我们提出，Tat通过演化出这些独特特性，劫持精准的基因组区域，利用与HIV基因组调控模式显著不同的意料之外的调控机制来控制细胞转录。本研究还证实，Tat可作为分子探针，用于解析转录调控的通用原则。整体实验设计：Tat组 vs. 绿色荧光蛋白（GFP）组