Structure of the HIV-1 Genome

描述（由申请人提供）：该项目将生物医学科学中的三个广泛重要的问题联系起来。首先，人类免疫缺陷病毒（艾滋病毒）感染了3 300万人，每年大约有300万新感染者。我们的实验室最近开发了一种HIV-1病毒整个RNA基因组的整体结构和二级结构模型。这项工作揭示了许多以前未被识别，但进化上保守的RNA结构。进一步完善完整的HIV基因组结构和鉴定基因组中的蛋白质-RNA相互作用，对于确定抗逆转录病毒药物开发的新靶点和途径具有重要意义。其次，病毒篡夺了所有生物体中存在的遗传指令。我们在HIV-1基因组中发现的结构化RNA调控元件似乎影响剪接、蛋白质翻译、逃避宿主细胞防御以及药物结合的可及性。HIV-1 RNA基因组中编码的信息密度非常大，似乎是遗传密码的一个关键组成部分，我们目前对它的了解还很有限。因此，拟议的研究计划将提高我们对所有生物学中基因调控基本原理的理解。第三，基本上所有的RNA分子只有在折叠成特定的二级（和三级）结构后才能在生物学中发挥作用。由PI实验室发明的SHAPE（选择性引物延伸分析的2 '-羟基酰化）技术，现在可以分析几乎每个位置上任意大小的RNA和蛋白质结合的局部核苷酸环境。然而，数据分析仍然是劳动密集型的。我们试图简化数据处理步骤，使任意完整的大RNA的简便和全面的功能分析成为可能。因此，我们将与HIV生物学和生物信息学专家合作，实现以下目标：（1）分析另外两种HIV-1相关病毒的完整基因组结构，即来自黑猩猩的猿免疫缺陷病毒（SIVcpz）和来自恒河猴的猴免疫缺陷病毒（SIVmac）。(2)分析完整的HIV-1基因组，因为它存在于未成熟和成熟颗粒中的真实HIV-1病毒粒子内。(3)创建一个平台独立的、用户友好的软件，用于高通量SHAPE信息的全自动分析。所有技术进步和艾滋病毒基因组数据集将免费提供给生物医学科学界。

DESCRIPTION (provided by applicant): This project links three broadly important problems in biomedical science. First, the human immunodeficiency virus (HIV) infects 33 million individuals with roughly 3 million new infections per year. Our laboratory has recently developed a model for the overall architecture and secondary structure of the entire RNA genome for one HIV-1 virus. This work revealed numerous previously unrecognized, but evolutionarily conserved, RNA structures. Further refinement of complete HIV genome structures and identification of protein-RNA interactions in the genome hold significant promise for identifying novel targets and pathways for antiretroviral drug development. Second, viruses usurp the genetic instructions present in all living organisms. Structured RNA regulatory elements that we have discovered in the HIV-1 genome appear to influence splicing, protein translation, evasion of host cell defenses, and accessibility towards drug binding. The extraordinary density of information encoded in the HIV-1 RNA genome appears to represent a key component of the genetic code, one that we understand poorly at present. The proposed research program will therefore enhance our understanding of the fundamental principles that govern gene regulation in all of biology. Third, essentially all RNA molecules function in biology only after they fold into specific secondary (and tertiary) structures. SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) technology, invented in the PI's laboratory, now makes it possible to analyze the local nucleotide environment at nearly every position for RNAs of arbitrary size and as bound by proteins. However, data analysis remains labor-intensive. We seek to streamline the data processing steps to make possible facile and comprehensive functional analyses of arbitrary intact large RNAs. In collaboration with experts in HIV biology and in bioinformatics, we will therefore tackle the following Aims: (1) Analyze the structures of the complete genomes of two additional HIV-1 related viruses, the simian immunodeficiency virus from chimpanzees (SIVcpz) and from the rhesus macaque (SIVmac). (2) Analyze the complete HIV-1 genome, as it exists inside authentic HIV-1 virions in both immature and mature particles. (3) Create a platform-independent, user-friendly software for fully automated analysis of high-throughput SHAPE information. All technology advances and HIV genome data sets will be made freely available to the biomedical science community.