Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria.
Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr Gasse 9, 1030 Vienna, Austria.
Genetics. 2023 Aug 31;225(1). doi: 10.1093/genetics/iyad135.
Efficient repair of DNA lesions is essential for the faithful transmission of genetic information between somatic cells and for genome integrity across generations. Plants have multiple, partially redundant, and overlapping DNA repair pathways, probably due to the less constricted germline and the inevitable exposure to light including higher energy wavelengths. Many proteins involved in DNA repair and their mode of actions are well described. In contrast, a role for DNA damage-associated RNA components, evident from many other organisms, is less well understood. Here, we have challenged young Arabidopsis thaliana plants with two different types of genotoxic stress and performed de novo assembly and transcriptome analysis. We identified three long noncoding RNAs (lncRNAs) that are lowly or not expressed under regular conditions but up-regulated or induced by DNA damage. We generated CRISPR/Cas deletion mutants and found that the absence of the lncRNAs impairs the recovery capacity of the plants from genotoxic stress. The genetic loci are highly conserved among world-wide distributed Arabidopsis accessions and within related species in the Brassicaceae group. Together, these results suggest that the lncRNAs have a conserved function in connection with DNA damage and provide a basis for mechanistic analysis of their role.
有效的 DNA 损伤修复对于体细胞间遗传信息的忠实传递以及跨代基因组完整性至关重要。植物具有多种部分冗余且重叠的 DNA 修复途径，这可能是由于植物的生殖细胞系限制较少，并且不可避免地会暴露在包括更高能量波长的光线下。许多参与 DNA 修复的蛋白质及其作用模式已得到很好的描述。相比之下，尽管许多其他生物体中都存在与 DNA 损伤相关的 RNA 成分，但它们的作用却知之甚少。在这里，我们用两种不同类型的致突变应激处理年轻的拟南芥植物，并进行了从头组装和转录组分析。我们鉴定了三个长非编码 RNA（lncRNA），它们在常规条件下表达水平较低或不表达，但在 DNA 损伤时上调或诱导表达。我们生成了 CRISPR/Cas 缺失突变体，并发现 lncRNA 的缺失会损害植物从致突变应激中恢复的能力。这些遗传基因座在全球分布的拟南芥品系以及在十字花科植物组中的相关物种中高度保守。这些结果表明，lncRNA 具有与 DNA 损伤相关的保守功能，并为它们的作用机制分析提供了基础。
