Background Alternative splicing is a key step in Human Immunodeficiency Virus type 1 (HIV-1) replication that is tightly regulated both temporally and spatially. More than 50 different transcripts can be generated from a single HIV-1 unspliced pre-messenger RNA (pre-mRNA) and a balanced proportion of unspliced and spliced transcripts is critical for the production of infectious virions. Understanding the mechanisms involved in the regulation of viral RNA is therefore of potential therapeutic interest. However, monitoring the regulation of alternative splicing events at a transcriptome-wide level during cell infection is challenging. Here we used the long-read cDNA sequencing developed by Oxford Nanopore Technologies (ONT) to explore in a quantitative manner the complexity of the HIV-1 transcriptome regulation in infected primary CD4+ T cells. Results ONT reads mapping to the viral genome proved sufficiently long to span all possible splice junctions, even distant ones, and to be assigned to a total of 150 exon combinations. Fifty-three viral RNA isoforms, including 14 new ones were further considered for quantification. Relative levels of viral RNAs determined by ONT sequencing showed a high degree of reproducibility, compared favourably to those produced in previous reports and highly correlated with quantitative PCR (qPCR) data. To get further insights into alternative splicing regulation, we then compiled quantifications of splice site (SS) usage and transcript levels to build “splice trees”, a quantitative representation of the cascade of events leading to the different viral isoforms. This approach allowed visualizing the complete rewiring of SS usages upon perturbation of SS D2 and its impact on viral isoform levels. Furthermore, we produced the first dynamic picture of the cascade of events occurring between 12 and 24 h of viral infection. In particular, our data highlighted the importance of non-coding exons in viral RNA transcriptome regulation. Conclusion ONT sequencing is a convenient and reliable strategy that enabled us to grasp the dynamic of the early splicing events modulating the viral RNA landscape in HIV-1 infected cells.

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感染早期 HIV-1 剪接事件的动态纳米孔长读长测序分析

背景 选择性剪接是 1 型人类免疫缺陷病毒 (HIV-1) 复制的关键步骤，在时间和空间上都受到严格调控。可以从单个 HIV-1 未剪接的前信使 RNA (pre-mRNA) 生成 50 多种不同的转录本，并且未剪接和剪接转录本的平衡比例对于感染性病毒粒子的产生至关重要。因此，了解参与调节病毒 RNA 的机制具有潜在的治疗意义。然而，在细胞感染期间在转录组范围内监测选择性剪接事件的调节具有挑战性。在这里，我们使用牛津纳米孔技术 (ONT) 开发的长读长 cDNA 测序以定量方式探索受感染的原代 CD4+ T 细胞中 HIV-1 转录组调控的复杂性。结果 ONT 读取映射到病毒基因组被证明足够长，可以跨越所有可能的剪接点，甚至是远处的剪接点，并分配给总共 150 个外显子组合。进一步考虑了 53 种病毒 RNA 异构体，包括 14 种新的异构体进行定量。通过 ONT 测序确定的病毒 RNA 的相对水平显示出高度的可重复性，与之前报告中产生的那些相比具有优势，并且与定量 PCR (qPCR) 数据高度相关。为了进一步了解选择性剪接调控，我们随后编制了剪接位点 (SS) 使用和转录水平的量化数据，以构建“剪接树”，这是导致不同病毒同种型的级联事件的量化表示。这种方法允许在 SS D2 扰动时可视化 SS 用法的完全重新布线及其对病毒同种型水平的影响。此外，我们制作了病毒感染 12 至 24 小时之间发生的级联事件的第一个动态图片。特别是，我们的数据强调了非编码外显子在病毒 RNA 转录组调控中的重要性。结论 ONT 测序是一种方便可靠的策略，使我们能够掌握调节 HIV-1 感染细胞中病毒 RNA 格局的早期剪接事件的动态。