Nuclear genetic regulation of the human mitochondrial transcriptome

Abstract

Mitochondria play important roles in cellular processes and disease, yet little is known about how the transcriptional regime of the mitochondrial genome varies across individuals and tissues. By analyzing >11,000 RNA-sequencing libraries across 36 tissue/cell types, we find considerable variation in mitochondrial-encoded gene expression along the mitochondrial transcriptome, across tissues and between individuals, highlighting the importance of cell-type specific and post-transcriptional processes in shaping mitochondrial-encoded RNA levels. Using whole-genome genetic data we identify 64 nuclear loci associated with expression levels of 14 genes encoded in the mitochondrial genome, including missense variants within genes involved in mitochondrial function (TBRG4, MTPAP and LONP1), implicating genetic mechanisms that act in trans across the two genomes. We replicate ~21% of associations with independent tissue-matched datasets and find genetic variants linked to these nuclear loci that are associated with cardio-metabolic phenotypes and Vitiligo, supporting a potential role for variable mitochondrial-encoded gene expression in complex disease.

Keywords: RNA sequencing; chromosomes; eQTL; expression; gene expression; genetics; genomics; human; mitochondria; mtRNA; transcriptome.

Figure 1.. Variation in the expression of mitochondrial-encoded genes across datasets.

(A) Hierarchical clustering of median expression levels per gene across all datasets where WBL = Whole Blood, SAD = Subcutaneous Adipose, LCL = Lymphoblastoid cell lines, SKN = Non sun exposed skin, SKE = Sun exposed skin, VAD = Visceral omentum adipose, ADG = Adrenal gland, AOR = Aorta, CAR = Coronary artery, TAR = Tibial artery, ACB = Anterior cingulate cortex (BA24) (Brain), CGB = Caudate basal ganglia (Brain), CHB = Cerebellar Hemisphere (Brain), CEB = Cerebellum (Brain), COB = Cortex (Brain), FCB = Frontal cortex (BA9) (Brain), HIB = Hippocampus (Brain), HYB = Hypothalamus (Brain), NAB = Nucleus accumbens (basal ganglia) (Brain), PBB = Putamen basal ganglia (Brain), BRE = Breast mammary tissue, SCO = Sigmoid colon, TCO = Transverse colon, GEJ = Gastroesophageal junction, EMC = Esophagus mucosa, EMS = Esophagus Muscularis, AAH = Atrial appendage (Heart), LVH = Left ventricle (Heart), LUN = Lung, SMU = Skeletal muscle, TNV = Tibial Nerve, PAN = Pancreas, SFI = Transformed fibroblasts, STO = Stomach, TES = Testes and THY = Thyroid, Multi-dataset tissues on the x-axis are shown in red (whole blood), orange (subcutaneous adipose), green (lymphoblastoid cell lines) and blue (non-sun exposed skin). (B) Standardized expression levels of each mitochondrial-encoded gene across all independent datasets, (C) Coefficient of variation across individuals for the expression levels of mitochondrial encoded genes and the top 1000 most highly expressed nuclear genes in all datasets. Range of coefficient of variation is restricted to between 0 and 1.5 as this contains the majority of the data.

Figure 2.. Associations between the expression of MTND1 and rs2304694 in whole blood data.

(A) Genome-wide association analysis for the expression of MTND1 in whole blood data from the discovery datasets (meta-analysis of CARTaGENE, TwinsUK and GTEx data), (B) Genome-wide association analysis for the expression of MTND1 in whole blood data from the replication dataset (NIMH data), (C) Expression of MTND1 (Log₁₀(TPM +1)) versus non-reference allele frequency of rs2304694 in the four independent whole blood datasets.

Figure 2—figure supplement 1.. QQ plots for associations between nuclear genetic variants and mitochondrial gene expression for discovery associations that replicate at the nominal 5% level.

Figure 3.. Replication and validation of significant associations between nuclear genetic variants and the expression of mitochondria-encoded genes.

(A) Discovery versus replication beta estimates for significant associations between nuclear genetic variation and mitochondrial gene expression detected in discovery data at FDR 5%, (B) Validation of the association between rs2304694 and the expression of MTND4 using quantitative PCR in LCLs. MTND4 mRNA expression levels are normalised to GAPDH (theoretical quantities).