The neglected genome

Mitochondria harbour some of the most critical functions of life [1,2,3]. As the site of ATP synthesis by oxidative phosphorylation, they are the primary energy-generating system in almost all eukaryotic cells and are central to programmed cell death. Mitochondria also play major roles in a broad range of other key processes such as the synthesis of amino acids, haem, nucleotides and lipids, ion homeostasis, cell proliferation and motility. It is of major evolutionary and functional significance that they carry their own small DNA genome—a legacy of the endosymbiosis that created mitochondria, and possibly the eukaryotic cell, some 1.5–2 billion years ago [4]. In humans, mitochondrial DNA (mtDNA) is a double-stranded circular molecule of 16.5 kilobase pairs that carries only 37 genes, 13 of which encode proteins.

The coordinated expression of the mitochondrial genome with the nuclear genome is essential for the functioning of eukaryotic cells [5]. This interaction is subject to epigenetic regulation because chromosome phosphorylation, acetylation and methylation are modulated by energy availability and redox state [6]. As a consequence, mitochondrial dysfunctions have pleiotropic effects in multicellular organisms and give rise to a large spectrum of defects [7,8,9,10].

The vast majority of proteins involved in mitochondrial biogenesis and function are encoded by the nuclear genome and imported into mitochondria as precursors. Yet the 13 proteins encoded by human mtDNA are crucial for life as they are essential subunits of the oxidative phosphorylation system [11,12,13]. Moreover, changes in their expression affect nuclear genes through pathways as yet poorly understood.

Complete functional genomic analyses must consider nuclear–mitochondrial interplay by describing genetic, epigenetic and expression profiles of both genomes in healthy and pathological conditions.

Mutations in mtDNA are associated with a wide range of severe diseases, preferentially affecting tissues with high energy demand. These diseases include specific metabolic conditions, but also ageing, various degenerative diseases, and probably fertility [14] and cancer [13].

The advent of next-generation sequencing technologies is profoundly revolutionizing several areas of biological research and providing unprecedented possibilities for functional genomic studies. Genome sequencing and expression profiling are now routinely performed at increasing economy and speed. Indeed, we are facing a flourishing of papers reporting large-scale analysis of genome variation in different populations and diseases, for example, the 1000 Genomes Project and the Cancer Genome Atlas, genome-wide associations studies (GWAS) for several diseases, as well as high-throughput expression profiling in different cell types and conditions.

However, despite the increasing evidence for the fundamental role of nuclear–mitochondrial communication in eukaryotic cell functions, the overwhelming majority of functional genomic studies largely neglect the mitochondrial contribution at the level of genome sequence in the detection of mutations or polymorphisms, and in gene expression profiling.

Commercial kits for genome-wide investigations neglect the tiny but crucial store of genetic material in mtDNA, and genome sequencing protocols sometimes involve steps designed to minimize ‘mitochondrial contamination’ [15]. For example, DNA enrichment systems for exome sequencing do not include probes targeting mitochondrial genes, thus ignoring variations and mutations in mtDNA [16]. Furthermore, although the necessary raw data are often available, for example, RNA-Seq data include mtDNA transcription products, most popular bioinformatics computer programs for transcriptome profiling do not take into account mitochondrially encoded transcripts. With the increased interest in understanding ‘missing heritability’ and epistatic interactions in GWAS studies, the lack of mtDNA markers ensures that ‘mito-nuclear’ epistases will be missed.

We strongly recommend that high-throughput investigations begin to integrate information from both mitochondrial and nuclear–cytosolic genetic systems to fully understand the behaviour of eukaryotic cells in health and disease. This integrative approach will open new avenues in studies focused on molecular evolution and on selective adaptation in eukaryotes as well as addressing the onset and treatment of degenerative and age-related diseases.