RNA dimerization is the noncovalent association of two human immunodeficiency virus-1 (HIV-1) genomes. It is a conserved step in the HIV-1 life cycle and assumed to be a prerequisite for binding to the viral structural protein Pr55^Gag during genome packaging. Here, we developed functional analysis of RNA structure-sequencing (FARS-seq) to comprehensively identify sequences and structures within the HIV-1 5′ untranslated region (UTR) that regulate this critical step. Using FARS-seq, we found nucleotides important for dimerization throughout the HIV-1 5′ UTR and identified distinct structural conformations in monomeric and dimeric RNA. In the dimeric RNA, key functional domains, such as stem-loop 1 (SL1), polyadenylation signal (polyA) and primer binding site (PBS), folded into independent structural motifs. In the monomeric RNA, SL1 was reconfigured into long- and short-range base pairings with polyA and PBS, respectively. We show that these interactions disrupt genome packaging, and additionally show that the PBS–SL1 interaction unexpectedly couples the PBS with dimerization and Pr55^Gag binding. Altogether, our data provide insights into late stages of HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging.

RNA 二聚化是两个人类免疫缺陷病毒 1 (HIV-1) 基因组的非共价关联​​。它是 HIV-1 生命周期中的一个保守步骤，被认为是与病毒结构蛋白 Pr55 ^{Gag结合的先决条件}在基因组包装过程中。在这里，我们开发了 RNA 结构测序 (FARS-seq) 的功能分析，以全面识别调节这一关键步骤的 HIV-1 5' 非翻译区 (UTR) 内的序列和结构。使用 FARS-seq，我们发现核苷酸对整个 HIV-1 5' UTR 的二聚化很重要，并在单体和二聚体 RNA 中识别出不同的结构构象。在二聚体 RNA 中，关键功能域，如茎环 1 (SL1)、聚腺苷酸化信号 (polyA) 和引物结合位点 (PBS)，折叠成独立的结构基序。在单体 RNA 中，SL1 被重新配置为分别与 polyA 和 PBS 进行长程和短程碱基配对。我们表明这些相互作用会破坏基因组包装，^堵嘴绑定。总而言之，我们的数据提供了对 HIV-1 生命周期后期的见解，以及对 RNA 二聚化和包装之间联系的机制解释。