Revealing the RNA-RNA interactome of the HIV-1 genome

项目总结/摘要 逆转录病毒，像许多RNA病毒一样，具有高突变率，允许快速的基因组进化来选择。 有益的宿主因子相互作用。近年来，非编码RNA（ncRNA）在宿主抗病毒中的重要性日益受到重视， 然而，许多RNA病毒也已经进化到利用宿主ncRNA， 为了他们自己的利益。事实上，已经鉴定了几种微RNA（miRNAs），其抑制细胞的复制。 哺乳动物的RNA病毒，而另一些则增加复制。重要的是要指出， 在很多情况下对病毒是有利的此外，逆转录病毒依赖于宿主 tRNA以引发其基因组RNA（gRNA）逆转录成双链前病毒DNA。这 基本的tRNA-gRNA相互作用先于逆转录病毒感染期间的所有酶催化过程。 宿主细胞此外，由tRNA的内切核酸裂解产生的tRNA衍生片段（tRF）具有 最近显示通过调节逆转录来抑制内源性逆转录病毒复制。由于 HIV-1对选择性压力的快速反应，很可能已经进化出了对RNA的反应机制， 介导的宿主过程;然而，HIV-1 gRNA核酸相互作用组的全面鉴定 缺乏在这里，我们的目标是测试总体假设，即HIV-1 gRNA已经进化出关键的RNA-RNA 相互作用，如替代构象，长程分子内相互作用和直接结合的主机 ncRNA以优化感染性。具体目的是（1）鉴定HIV-1 gRNA分子内碱基配对， 分子间宿主RNA相互作用和（2）测试HIV-1 RNA-RNA相互作用的生物学意义。

Project Summary/Abstract Retroviruses, like many RNA viruses, have high mutation rates, allowing rapid genome evolution to select for beneficial host factor interactions. Recently the importance of non-coding RNAs (ncRNAs) for host antiviral processes have been highlighted; however, many RNA viruses have also evolved to make use of host ncRNAs for their own benefit. Indeed, several microRNAs (miRNAs) have been identified that inhibit replication of mammalian RNA viruses while others increase replication. It is important to point out that repressed replication is likely to be advantageous to the virus in many instances. Furthermore, retroviruses are dependent on a host tRNA to prime reverse transcription of their genomic RNA (gRNA) into double-stranded proviral DNA. This fundamental tRNA-gRNA interaction precedes all enzyme-catalyzed processes during retroviral infection of a host cell. In addition, tRNA-derived fragments (tRFs) that result from endonucleolytic cleavage of tRNAs have recently been shown to inhibit endogenous retroviral replication by regulating reverse transcription. Due to the rapid response of HIV-1 to selective pressure, it is likely to have evolved mechanisms of responding to RNA- mediated host processes; however, comprehensive identification of the HIV-1 gRNA nucleic acid interactome is lacking. Here, we aim to test the overarching hypothesis that HIV-1 gRNA has evolved critical RNA-RNA interactions such as alternative conformations, long-range intra-molecular interactions and direct binding of host ncRNAs to optimize infectivity. The specific aims are to (1) identify HIV-1 gRNA intra-molecular base-pairing and inter-molecular host RNA interactions and (2) test the biological significance of HIV-1 RNA-RNA interactions.