Structure of the HIV-1 Genome

描述(由申请者提供)：这个项目联系了生物医学科学中三个广泛重要的问题。首先，人类免疫缺陷病毒(HIV)感染3300万人，每年约有300万新感染者。我们实验室最近为一种HIV-1病毒的整个RNA基因组的整体结构和二级结构开发了一个模型。这项工作揭示了许多以前没有被认识到的，但在进化上保守的RNA结构。进一步完善完整的艾滋病毒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的前景。其次，病毒篡夺了存在于所有生物体内的遗传指令。我们在HIV-1基因组中发现的结构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-1RNA基因组中编码的异常密集的信息似乎代表了遗传密码的一个关键组成部分，而我们目前对此知之甚少。因此，拟议的研究计划将加强我们对支配整个生物学中基因调控的基本原则的理解。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的实验室发明的Shape(由引物延伸分析的选择性2‘-羟基酰化)技术，现在使分析任意大小和蛋白质结合的RNA的几乎每个位置的局部核苷酸环境成为可能。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，使对任意完整的大RNA进行方便和全面的功能分析成为可能。因此，我们将与艾滋病毒生物学和生物信息学专家合作，实现以下目标：(1)分析另外两种与艾滋病毒-1相关的病毒--黑猩猩免疫缺陷病毒(SIVcpz)和恒河猴免疫缺陷病毒(SIVmac)--的全基因组结构。(2)分析HIV-1全基因组，因为它存在于未成熟和成熟颗粒中的真实HIV-1病毒粒子中。(3)创建与平台无关、用户友好的软件，以实现高通量形状信息的全自动分析。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.