Abstract：
The human immunodeficiency virus (HIV-1) is highly dependent on a variety of host factors. Beside proteins, host RNA molecules are reported to aid HIV-1 replication and latency maintenance. Here, we implement multiple workflows of native RNA immunoprecipitation and sequencing (nRIPseq) to determine direct host RNA interaction partners of all 18 HIV-1 (poly)proteins. We identify 1,727 HIV-1 protein - human RNA interactions in the Jurkat cell line and 1,558 interactions in SupT1 cells for a subset of proteins, and discover distinct cellular pathways that seem to be used or controlled by HIV-1 on the RNA level: Tat binds mRNAs of proteins involved in the super elongation complex (AFF1-4, Cyclin-T1). Correlation of the interaction scores (based on binding abundancy) allows identifying the highest confidence interactions, for which we perform a small-scale knockdown screen that leads to the identification of three HIV-1 protein binding RNA interactors involved in HIV-1 replication (AFF2, H4C9 and RPLP0).
摘要：
人类免疫缺陷病毒(HIV-1)高度依赖于多种宿主因子。除了蛋白质，据报道，宿主RNA分子有助于HIV-1复制和潜伏期维持。这里,我们实施了天然RNA免疫沉淀和测序(nRIPseq)的多个工作流程,以确定所有18种HIV-1(聚)蛋白的直接宿主RNA相互作用伴侣.我们确定了Jurkat细胞系中的1,727个HIV-1蛋白-人类RNA相互作用和SupT1细胞中的1,558个相互作用的一部分蛋白质，并发现似乎在RNA水平上由HIV-1使用或控制的不同细胞途径：Tat结合参与超延伸复合物（AFF1-4，Cyclin-T1）的蛋白质的mRNA。相互作用得分的相关性(基于结合丰度)允许识别最高置信度的相互作用，为此，我们进行了小规模敲除筛选，从而鉴定了参与HIV-1复制的三种HIV-1蛋白结合RNA相互作用因子（AFF2，H4C9和RPLP0）。
