Mitochondrial DNA background significantly alters transcriptional response to a various diets in mice

Mutations in the mitochondrial DNA (mtDNA) have been proposed to be essential for metabolic adaptation, and because metabolism is intrinsically associated with multiple disease states, including obesity, we hypothesized that changes in the mtDNA would significantly influence adiposity and gene expression in response to diet. To test these predictions we used Mitochondrial-Nuclear eXchange mice, which have nuclear and mitochondrial genomes that have been exchanged from different M. musculus strains. Overall design: Purpose: Mutations in the mitochondrial DNA (mtDNA) have been proposed to be essential for metabolic adaptation, and because metabolism is intrinsically associated with multiple disease states, including obesity, we hypothesized that changes in the mtDNA would significantly influence adiposity and gene expression in response to diet. To test these predictions we used Mitochondrial-Nuclear eXchange mice, which have nuclear and mitochondrial genomes that have been exchanged from different M. musculus strains. Methods: Wild type (C57BL6/J – C57n:C57mt and C3H/HeN - C3Hn:C3Hmt) and MNX (C57n:C3Hmt and C3Hn:C57mt) mouse were weaned with Chor diet and continued with Chow or changed to high-fat diet from 6 to 12-13 weeks of age. RNA samples were isolated from white adipose tissues collected from epididymal (eWAT) and inguinal (iWAT) fat, representing visceral and subcutaneous fat depots, respectively with RNeasy kit (Qiagen). Reverse transcribed cDNA libraries were sequenced with an Illumina HiSeq 2000. Read mapping was conducted with a proprietary algorithm by Expression Analysis (www.q2labsolutions.com), and read counts were used as input for differential expression analysis in DESeq2 version 1.10.1, using default settings. Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (build mm9). Transcriptional changes were interrogated for 961 genes previously reported to be associated with fat metabolism and 29,209 genes representing the entire mouse transcriptome. These results show that the C57 mtDNA increased the number of DE genes in response to high fat diet in mice harboring the C3H nuclear genome (209% increase; C3Hn:C57mt versus C3Hn:C3Hmt, 165/79) and the C3H mtDNA decreased response in animals carrying the C57 nucleus (46% decrease; C57n:C3Hmt versus C57n:C57mt, 112/206) in eWAT (Figure 2B). Similarly, the high fat diet resulted in 25 and 231 DE genes in the C3Hn:C3Hmt and C3Hn:C57mt iWAT, respectively, and 344 and 143 DE genes in C57n:C57mt and C57n:C3Hmt iWAT. This corresponded to a 924% increase in the number of DE genes responding to high fat diet C3Hn:C57mt versus C3Hn:C3Hmt, and a decreased response (58% decrease) in C57n:C3Hmt relative to C57n:C57mt iWAT. Further analysis showed that each MNX and corresponding wild-type shared and had distinct DE genes in eWAT and iWAT. Conclusions: Results also show that the degree of transcriptional response influenced by the mtDNA can vary based upon the type of adipose tissue, suggesting that mtDNA background can have varying effects on the number of nuclear genes differentially responding to stimuli, depending upon tissue and location.

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Dunham-Snary KJ, Sandel MW, Sammy MJ, Westbrook DG, Xiao R, McMonigle RJ, Ratcliffe WF, Penn A, Young ME, Ballinger SW