Mitochondria are ancient endosymbiotic organelles crucial to eukaryotic growth and metabolism. The mammalian mitochondrial genome encodes for 13 mitochondrial proteins, and the remaining mitochondrial proteins are encoded by the nuclear genome. Little is known about how coordination between the expression of the two sets of genes is achieved. Correlation analysis of RNA-seq expression data from large publicly available datasets is a common method to leverage genetic diversity to infer gene co-expression modules. Here we use this method to investigate nuclear-mitochondrial gene expression coordination. We identify a pitfall in correlation analysis that results from the large variation in the proportion of transcripts from the mitochondrial genome in RNA-seq data. Commonly used normalisation techniques based on total read counts, such as FPKM or TPM, produce artefactual negative correlations between mitochondrial- and nuclear-encoded transcripts. This also results in artefactual correlations between pairs of nuclear-encoded genes, with important consequences for inferring co-expression modules beyond mitochondria. We show that these effects can be overcome by normalizing using the median-ratio normalisation (MRN) or trimmed mean of M values (TMM) methods. Using these normalisations, we find only weak and inconsistent correlations between mitochondrial and nuclear-encoded mitochondrial genes in the majority of healthy human tissues from the GTEx database. We show that a subset of healthy tissues with high expression of NF-κB show significant coordination, suggesting a role for NF-κB in ensuring balanced expression between mitochondrial and nuclear genes. Contrastingly, most cancer types show robust coordination of nuclear and mitochondrial OXPHOS gene expression, identifying this as a feature of gene regulation in cancer.

中文翻译：

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恶性肿瘤和 NF-κB 信号传导加强线粒体和核编码的氧化磷酸化基因表达之间的协调

线粒体是古老的内共生细胞器，对真核生物的生长和代谢至关重要。哺乳动物线粒体基因组编码13种线粒体蛋白，其余线粒体蛋白由核基因组编码。关于两组基因的表达之间的协调是如何实现的，人们知之甚少。对来自大型公开数据集的 RNA-seq 表达数据进行相关性分析是利用遗传多样性推断基因共表达模块的常用方法。在这里，我们使用这种方法来研究核线粒体基因表达协调。我们发现了相关分析中的一个陷阱，该陷阱是由于 RNA-seq 数据中线粒体基因组转录本比例的巨大变化造成的。基于总读取计数的常用标准化技术（例如 FPKM 或 TPM）会在线粒体和核编码转录本之间产生人为的负相关性。这也导致核编码基因对之间的人为相关性，对于推断线粒体以外的共表达模块具有重要影响。我们证明，可以通过使用中值比归一化 (MRN) 或 M 值修整平均值 (TMM) 方法进行归一化来克服这些影响。使用这些标准化，我们从 GTEx 数据库中发现大多数健康人体组织中线粒体和核编码线粒体基因之间的相关性很弱且不一致。我们发现，NF-κB 高表达的健康组织子集表现出显着的协调性，这表明 NF-κB 在确保线粒体和核基因之间平衡表达方面发挥着作用。相比之下，大多数癌症类型显示出核和线粒体 OXPHOS 基因表达的强大协调性，将其确定为癌症基因调控的一个特征。