Schultz Samantha, Miles Jacob, Dwyer Will, MacVeigh-Fierro Daniel, Muller Mandy
bioRxiv. 2025 Jun 5:2025.06.05.657986. doi: 10.1101/2025.06.05.657986.
RNA turnover is critical for regulating cellular homeostasis, with nuclear export representing a key step in mRNA fate. During infection by Kaposi's Sarcoma-associated Herpesvirus (KSHV), widespread mRNA decay is mediated by the viral endonuclease SOX, which depletes cytoplasmic transcripts and induces secondary nuclear RNA processing defects. One such defect includes transcript hyperadenylation, which promotes nuclear retention and decay. However, a subset of mRNAs escapes both SOX degradation and nuclear retention, raising questions about their export mechanisms. Here, we investigate how KSHV infection impacts mRNA poly(A) tail length and nuclear export dynamics using poly(A)-sequencing in KSHV-positive cells. Our data confirm a global increase in poly(A) tail length during KSHV infection, yet we identified a group of hyperadenylated transcripts that remain localized in the cytoplasm, suggesting active evasion of nuclear retention. Notably, we focused on interleukin-6 (IL-6), an mRNA known to escape SOX-mediated decay. Using G/I tailing and sPAT assays, we show that IL-6 is hyperadenylated yet, exported. We demonstrate that its export is dependent upon the CRM1 nuclear export pathway, rather than through the canonical NXF1-NXT1 pathway. Inhibition of CRM1 impairs IL-6 nuclear export and reduces steady-state mRNA levels, implicating CRM1 export in the stabilization of this transcript. Our findings reveal a previously unrecognized mechanism by which select host mRNAs like IL-6, bypass KSHV-imposed nuclear export block, thereby preserving their cytoplasmic function during infection. This study highlights viral manipulation of RNA processing and export pathways as a critical determinant of transcript fate and identifies CRM1 as a key mediator of selective transcript preservation during KSHV infection.
Kaposi's sarcoma-associated herpesvirus (KSHV) globally disrupts host gene expression by inducing host shutoff which triggers a global repression of the host transcriptome via widespread RNA decay, RNA, nascent transcript hyperadenylation and nuclear export blocks, yet a subset of transcripts escape this repression. This study reveals that despite acquiring long poly(A) tails, select host mRNAs such as IL-6 evade nuclear retention by using the alternative CRM1-dependent export pathway and remain stable in the cytoplasm. These findings challenge the prevailing model that hyperadenylation alone dictates nuclear decay and uncover a selective mechanism by which crucial host transcripts bypass KSHV-mediated gene repression. Understanding this selective escape provides new insights into host-virus interactions and highlights CRM1 as a potential therapeutic target in KSHV-associated diseases.
RNA 周转对于调节细胞内稳态至关重要，核输出是 mRNA 命运的关键步骤。在卡波西肉瘤相关疱疹病毒（KSHV）感染期间，广泛的 mRNA 衰变由病毒核酸内切酶 SOX 介导，它消耗细胞质转录本并诱导继发性核 RNA 加工缺陷。其中一个缺陷包括转录本超腺苷酸化，这会促进核滞留和衰变。然而，一部分 mRNA 既能逃脱 SOX 降解又能逃脱核滞留，这引发了关于它们输出机制的问题。在这里，我们使用 KSHV 阳性细胞中的聚腺苷酸测序来研究 KSHV 感染如何影响 mRNA 聚（A）尾长度和核输出动力学。我们的数据证实了 KSHV 感染期间聚（A）尾长度的总体增加，但我们鉴定出一组超腺苷酸化的转录本仍定位在细胞质中，这表明它们能主动逃避核滞留。值得注意的是，我们聚焦于白细胞介素 -6（IL -6），一种已知能逃脱 SOX 介导衰变的 mRNA。使用 G/I 加尾和 sPAT 分析，我们表明 IL -6 虽超腺苷酸化但仍能输出。我们证明其输出依赖于 CRM1 核输出途径，而非通过经典的 NXF1 - NXT1 途径。抑制 CRM1 会损害 IL -6 的核输出并降低稳态 mRNA 水平，这表明 CRM1 输出参与了该转录本的稳定。我们的发现揭示了一种先前未被认识的机制，通过该机制像 IL -6 这样的特定宿主 mRNA 绕过 KSHV 施加的核输出阻滞，从而在感染期间保留其细胞质功能。这项研究强调了病毒对 RNA 加工和输出途径的操纵是转录本命运的关键决定因素，并确定 CRM1 是 KSHV 感染期间选择性转录本保留的关键介质。
卡波西肉瘤相关疱疹病毒（KSHV）通过诱导宿主关闭来全局破坏宿主基因表达，宿主关闭通过广泛的 RNA 衰变、RNA、新生转录本超腺苷酸化和核输出阻滞触发宿主转录组的全局抑制，但仍有一部分转录本逃脱这种抑制。这项研究表明，尽管获得了长聚（A）尾，但像 IL -6 这样的特定宿主 mRNA 通过使用依赖于 CRM1 的替代输出途径逃避核滞留，并在细胞质中保持稳定。这些发现挑战了仅超腺苷酸化决定核衰变的主流模型，并揭示了一种关键宿主转录本绕过 KSHV 介导的基因抑制的选择性机制。理解这种选择性逃逸为宿主 - 病毒相互作用提供了新的见解，并强调 CRM1 是 KSHV 相关疾病的潜在治疗靶点。
