RNA damage compartmentalization by DHX9 granules. RNA damage compartmentalization by DHX9 granules

Cell division ensures that both genetic information and non-genetic contents are inherited by daughter cells. Whereas considerable detail has been learned about the processing of intact or damaged DNA during the cell cycle (Branzei & Foiani, 2008; Klaasen et al., 2022),(Bakhoum & Cantley, 2018),(Hustedt & Durocher, 2016), how daughter cells deal with other forms of inherited damage is unknown. Here we identified a special kind of cytoplasmic granules responsible for the compartmentalisation of parental RNA damage. We found that ultraviolet (UV)-induced RNA, but not DNA, damage triggered assembly of this unique type of granules characterized by the presence of RNA helicase DHX9. By developing a novel methodology, FANCI, we discovered that DHX9 granules are enriched in damaged intron RNA and pre-mRNA-binding proteins, which is in contrast to other classical stress granules (SGs) that are composed of mature mRNA. Intron damage impeded proper splicing and intron decay, and induced generation of circRNA and dsRNA in the granules. Moreover, we showed that intron damage induced DHX9 granules assembled specifically in postmitotic daughter cells and triggered a cellular dsRNA immune response. Condensation with dsRNA is crucial for DHX9 localization to the granules and the modulation of dsRNA in these granules by DHX9 was crucial for daughter cell survival. Our observations revealed that DHX9 granules constitute a dedicated non-membrane-bound cytoplasmic compartment that protects daughter cells from parental damaged RNA. Overall design: We generated total RNA-Seq profiles of Hela cells and stress granules treated with different stresses. We performed FLASH to analyze endogenous RNA binding sites of DHX9 in HeLa cells.

细胞分裂可确保子代细胞同时继承遗传信息与非遗传物质。尽管学界已对细胞周期中完整或受损DNA的加工机制取得诸多深入认识（Branzei & Foiani, 2008; Klaasen et al., 2022; Bakhoum & Cantley, 2018; Hustedt & Durocher, 2016），但子代细胞如何应对其他类型的继承性损伤仍不明晰。本研究中，我们鉴定出一类特殊的细胞质颗粒，其功能是分隔母源RNA损伤产物。我们发现，紫外线（ultraviolet, UV）诱导的RNA（而非DNA）损伤可触发这类以RNA解旋酶DHX9为标志性特征的独特颗粒的组装。通过开发一种名为FANCI的全新实验方法，我们发现DHX9颗粒富集有受损内含子RNA与前体mRNA（pre-mRNA）结合蛋白，这与由成熟mRNA构成的经典应激颗粒（stress granules, SGs）截然不同。内含子损伤会阻碍正常剪接与内含子降解，并诱导颗粒内环状RNA（circRNA）与双链RNA（double-stranded RNA, dsRNA）的生成。此外，我们证实内含子损伤诱导的DHX9颗粒仅在有丝分裂后子代细胞中组装，并可触发细胞内dsRNA免疫应答。与dsRNA的凝聚过程对于DHX9定位于颗粒至关重要，而DHX9对这些颗粒内dsRNA的调控则对子代细胞的存活不可或缺。本研究结果表明，DHX9颗粒是一类专门的非膜包被细胞质区室，可保护子代细胞免受母源受损RNA的侵害。实验整体设计：我们对经不同应激处理的海拉（HeLa）细胞以及应激颗粒进行了总RNA测序（total RNA-Seq）谱分析；此外，我们采用FLASH技术分析了海拉细胞内DHX9的内源性RNA结合位点。