Integrative functional genomics of DNA virus infections

Depth-DV的一个中心目标是确定DNA病毒感染之间宿主和病毒基因调控的共同机制和差异。为此，我们将利用由各个深度DV项目产生的功能基因组测序数据来满足其特定的项目目标。这些数据为Z01提供了丰富的资源，用于超越单个项目目标的比较分析，并整合了深度DV项目和不同的功能基因组分析。为了促进数据整合，我们将开发标准化的分析工作流程、数据和分析共享平台(深度DV中心)以及挖掘公共数据的方法。这将使我们能够使用深度DV内部和公共数据对不同DNA病毒的转录和表观遗传调控进行广泛的分析。我们将开发方法来研究和比较不同DNA病毒感染期间转录和表观遗传的变化及其相互作用，以及感染前的表观遗传启动以实现快速转录反应。此外，我们还将重点介绍启动子近端RNA聚合酶II(RNAPII)的暂停、提前转录终止及其在HSV-1和其他DNA病毒感染中的相互作用。这些研究问题源于对HSV-1感染中广泛存在的RNAPII暂停丢失和多聚腺苷酸化位点过早转录终止的初步观察。后者此前曾被认为与CDK9激酶的抑制有关。值得注意的是，CDK9是从启动子释放暂停的RNAPII所必需的，它的抑制作用阻止了处于暂停状态的RNAPII。因此，Z01将解决CDK9在HSV-1感染过程中的异质性作用，以及已知与CDK9相互作用的HSV-1即刻早期蛋白ICP22的作用。所有结果都将纳入Depth-DV中心，该中心将为在假定的第二个资助期建立DNA病毒感染公共知识库奠定基础。

A central aim of DEEP-DV is the identification of common mechanisms and differences in host and viral gene regulation between DNA virus infections. For this purpose, we will leverage functional genomics sequencing data generated by the individual DEEP-DV projects to address their specific project objectives. These data provide a rich resource for Z01 for comparative analyses that go beyond the individual project aims and integrate across DEEP-DV projects and different functional genomics assays. To facilitate data integration, we will develop standardized analysis workflows, a data and analysis sharing platform (the DEEP-DV Hub) as well as approaches for mining public data. This will allow us to perform an extensive analysis of transcriptional and epigenetic regulation across different DNA viruses using both DEEP-DV-internal and public data. We will develop methods to investigate and compare transcriptional and epigenetic changes and their interplay during infection with different DNA viruses as well as epigenetic priming prior to infection for rapid transcriptional responses. In addition, we will focus on promoter proximal RNA Polymerase II (RNAPII) pausing, premature transcription termination and their interplay in HSV-1 and other DNA virus infections. These research questions arise from preliminary observations on a widespread RNAPII pausing loss in HSV-1 infection and premature transcription termination at polyadenylation sites. The latter has previously been associated with inhibition of the CDK9 kinase. Notably, CDK9 is required for the release of paused RNAPII from the promoter and its inhibition arrests RNAPII in a paused state. Thus, Z01 will resolve the heterogeneous roles of CDK9 during HSV-1 infection as well as the role of the HSV-1 immediate-early protein ICP22, which is known to interact with CDK9. All results will be incorporated into the DEEP-DV Hub, which will provide the foundation for a public knowledgebase on DNA virus infections pursued in a putative second funding period.