Mitochondrial DNA Haplotypes Define Gene Expression Patterns in Pluripotent and Differentiating Embryonic Stem Cells

Abstract

Mitochondrial DNA haplotypes are associated with various phenotypes, such as altered susceptibility to disease, environmental adaptations, and aging. Accumulating evidence suggests that mitochondrial DNA is essential for cell differentiation and the cell phenotype. However, the effects of different mitochondrial DNA haplotypes on differentiation and development remain to be determined. Using embryonic stem cell lines possessing the same Mus musculus chromosomes but harboring one of Mus musculus, Mus spretus, or Mus terricolor mitochondrial DNA haplotypes, we have determined the effects of different mitochondrial DNA haplotypes on chromosomal gene expression, differentiation, and mitochondrial metabolism. In undifferentiated and differentiating embryonic stem cells, we observed mitochondrial DNA haplotype-specific expression of genes involved in pluripotency, differentiation, mitochondrial energy metabolism, and DNA methylation. These mitochondrial DNA haplotypes also influenced the potential of embryonic stem cells to produce spontaneously beating cardiomyocytes. The differences in gene expression patterns and cardiomyocyte production were independent of ATP content, oxygen consumption, and respiratory capacity, which until now have been considered to be the primary roles of mitochondrial DNA. Differentiation of embryonic stem cells harboring the different mitochondrial DNA haplotypes in a 3D environment significantly increased chromosomal gene expression for all haplotypes during differentiation. However, haplotype-specific differences in gene expression patterns were maintained in this environment. Taken together, these results provide significant insight into the phenotypic consequences of mitochondrial DNA haplotypes and demonstrate their influence on differentiation and development. We propose that mitochondrial DNA haplotypes play a pivotal role in the process of differentiation and mediate the fate of the cell. STEM CELLS 2013;31:703-716 Disclosure of potential conflicts of interest is found at the end of this article.

The Cytoplasm Affects the Epigenome in Drosophila melanogaster

“…The previously elusive molecular mechanisms uncovered here are likely candidates to mediate the documented mito-nuclear effects on the expression of health and life history traits such as longevity and reproductive success. Our findings support previous suggestions [9,12,[29][30][31][32]48] that epigenetic changes may be involved in the phenotypic effects of mito-nuclear interactions and provide a hypothesis as to why histone methylation was correlated to altered development in cattle embryos after mitochondrial replacement [29].…”

“…A haplotype-specific influence of mitochondrial metabolism on nuclear gene expression has been outlined for ageing, cancer, and other diseases [9] as well as for evolutionary processes [18,20,22,34]. Our study now indicates that cytoplasmatically mediated modifications of the nuclear epigenome should also be considered as possible regulators of these effects on downstream components of health [12,[29][30][31]. The previously elusive molecular mechanisms uncovered here are likely candidates to mediate the documented mito-nuclear effects on the expression of health and life history traits such as longevity and reproductive success.…”

“…Mitochondrial function is largely dependent on the nuclear genome, first and foremost due to the fact that the vast majority of proteins present in mitochondria are nuclear-encoded. However, studies have also shown or suggested that mitochondria can influence nuclear gene expression and might be involved in the epigenetic regulation of the nuclear genome [9,12,17,[28][29][30][31][32]. For instance, depleting mitochondria in cultured human kidney cells caused changes in nuclear DNA methylation, an important bearer of epigenetic information [33].…”

The mitochondrial side of epigenetics

“…MtDNA haplotypes also affect nDNA gene expression, cell differentiation, and mitochondrial metabolism. Interestingly, an mtDNA haplotype-specific expression of genes involved in pluripotency, differentiation, mitochondrial energy metabolism, and DNA methylation has been observed in undifferentiated and differentiating embryonic stem cells (49). Furthermore, mtDNA methylation and copy number are sensitive to some mitochondria toxicants (13), highlighting the role of mtDNA as an environmental biosensor.…”

The rise of mitochondria in medicine

“…In addition, different mtDNA haplogroups that confer disease risk have also been associated with different gene expression profiles in stem cells (Kelly et al, 2013) and cytoplasmic hybrid cells (Kenney et al, 2014). This demonstrates that both pathogenic defects such as the m.3243A>G point mutation, as well as evolutionary defined and combinations of mtDNA single nucleotide polymorphisms (i.e., haplogroups) generate signals that modulate the expression of nuclear genes.…”