Vandiver Amy R, Herbst Allen, Stothard Paul, Wanagat Jonathan
Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, California 90095, USA.
Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, California 90073, USA.
Genome Res. 2025 Jan 22;35(1):55-65. doi: 10.1101/gr.279072.124.
Although it is well understood that mitochondrial DNA (mtDNA) deletion mutations cause incurable diseases and contribute to aging, little is known about the transcriptional products that arise from these DNA structural variants. We hypothesized that mitochondrial genomes containing deletion mutations express chimeric mitochondrial RNAs. To test this, we analyzed human and rat RNA sequencing data to identify, quantitate, and characterize chimeric mitochondrial RNAs. We observe increased chimeric mitochondrial RNA frequency in samples from patients with mitochondrial genetic diseases and in samples from aged humans. The spectrum of chimeric mitochondrial transcripts reflects the known pattern of mtDNA deletion mutations. To test the hypothesis that mtDNA deletions induce chimeric RNA transcripts, we treated 18 month old and 34 month old rats with guanidinopropionic acid to induce high levels of skeletal muscle mtDNA deletion mutations. With mtDNA deletion induction, we demonstrate that the chimeric mitochondrial transcript frequency also increases and correlates strongly with an orthogonal DNA-based mutation assay performed on identical samples. Further, we show that the frequency of chimeric mitochondrial transcripts predicts expression of both nuclear and mitochondrial genes central to mitochondrial function, demonstrating the utility of these events as metrics of age-induced metabolic change. Mapping and quantitation of chimeric mitochondrial RNAs provide an accessible, orthogonal approach to DNA-based mutation assays, offer a potential method for identifying mitochondrial pathology in widely accessible data sets, and open a new area of study in mitochondrial genetics and transcriptomics.
虽然人们很清楚线粒体DNA（mtDNA）缺失突变会导致无法治愈的疾病并促进衰老，但对于这些DNA结构变异产生的转录产物却知之甚少。我们推测，含有缺失突变的线粒体基因组会表达嵌合线粒体RNA。为了验证这一点，我们分析了人类和大鼠的RNA测序数据，以识别、定量和表征嵌合线粒体RNA。我们观察到，线粒体遗传疾病患者样本和老年人类样本中的嵌合线粒体RNA频率增加。嵌合线粒体转录本的谱反映了已知的mtDNA缺失突变模式。为了验证mtDNA缺失会诱导嵌合RNA转录本的假设，我们用胍基丙酸处理18个月大和34个月大的大鼠，以诱导高水平的骨骼肌mtDNA缺失突变。随着mtDNA缺失的诱导，我们证明嵌合线粒体转录本频率也会增加，并且与对相同样本进行的基于DNA的正交突变检测密切相关。此外，我们表明嵌合线粒体转录本的频率可预测线粒体功能核心的核基因和线粒体基因的表达，证明了这些事件作为年龄诱导的代谢变化指标的实用性。嵌合线粒体RNA的定位和定量为基于DNA的突变检测提供了一种可及的正交方法，为在广泛可及的数据集中识别线粒体病理学提供了一种潜在方法，并开辟了线粒体遗传学和转录组学的一个新研究领域。
