title: Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system.
abstract: BACKGROUND
  Transcriptional control of mitochondrial metabolism is essential for cellular function. A better understanding of this process will aid the elucidation of mitochondrial disorders, in particular of the many genetically unsolved cases of oxidative phosphorylation (OXPHOS) deficiency. Yet, to date only few studies have investigated nuclear gene regulation in the context of OXPHOS deficiency. In this study we performed RNA sequencing of two control and two complex I-deficient patient cell lines cultured in the presence of compounds that perturb mitochondrial metabolism: chloramphenicol, AICAR, or resveratrol. We combined this with a comprehensive analysis of mitochondrial and nuclear gene expression patterns, co-expression calculations and transcription factor binding sites.
  
  
  RESULTS
  Our analyses show that subsets of mitochondrial OXPHOS genes respond opposingly to chloramphenicol and AICAR, whereas the response of nuclear OXPHOS genes is less consistent between cell lines and treatments. Across all samples nuclear OXPHOS genes have a significantly higher co-expression with each other than with other genes, including those encoding mitochondrial proteins. We found no evidence for complex-specific mRNA expression regulation: subunits of different OXPHOS complexes are similarly (co-)expressed and regulated by a common set of transcription factors. However, we did observe significant differences between the expression of nuclear genes for OXPHOS subunits versus assembly factors, suggesting divergent transcription programs. Furthermore, complex I co-expression calculations identified 684 genes with a likely role in OXPHOS biogenesis and function. Analysis of evolutionarily conserved transcription factor binding sites in the promoters of these genes revealed almost all known OXPHOS regulators (including GABP, NRF1/2, SP1, YY1, E-box factors) and a set of novel candidates (ELK1, KLF7, SP4, EHF, ZNF143, and TEL2).
  
  
  CONCLUSIONS
  OXPHOS genes share an expression program distinct from other genes encoding mitochondrial proteins, indicative of targeted nuclear regulation of a mitochondrial sub-process. Within the subset of OXPHOS genes we established a difference in expression between mitochondrial and nuclear genes, and between nuclear genes encoding subunits and assembly factors. Most transcription regulators of genes that co-express with complex I are well-established factors for OXPHOS biogenesis. For the remaining six factors we here suggest for the first time a link with transcription regulation in OXPHOS deficiency.
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands. Robin.vanderLee@radboudumc.nl.
authors.forename: Robin
authors.initials: R
authors.lastname: van der Lee
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands. radek.szklarczyk@maastrichtuniversity.nl.|Department of Clinical Genetics, Unit Clinical Genomics, Maastricht University Medical Centre, 6200 MD, Maastricht, The Netherlands. radek.szklarczyk@maastrichtuniversity.nl.
authors.forename: Radek
authors.initials: R
authors.lastname: Szklarczyk
authors.affiliation: Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands. jan.smeitink@radboudumc.nl.
authors.forename: Jan
authors.initials: J
authors.lastname: Smeitink
authors.affiliation: Unit Clinical Genomics, Department of Genetics and Cell Biology, School for Growth and Development and for Cardiovascular Research, Maastricht University Medical Centre, Maastricht, The Netherlands. bert.smeets@maastrichtuniversity.nl.
authors.forename: Hubert J M
authors.initials: HJ
authors.lastname: Smeets
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands. Martijn.Huijnen@radboudumc.nl.
authors.forename: Martijn A
authors.initials: MA
authors.lastname: Huynen
authors.affiliation: Nijmegen Center for Mitochondrial Disorders, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, PO BOX 9101, 6500 HB, Nijmegen, The Netherlands. rutger.vogel@radboudumc.nl.
authors.forename: Rutger
authors.initials: R
authors.lastname: Vogel
mesh_terms: D001665:Binding Sites; D002460:Cell Line; D016000:Cluster Analysis; D042967:Electron Transport Complex I / Q000172:deficiency* / Q000235:genetics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D028361:Mitochondrial Diseases / Q000235:genetics* / Q000378:metabolism; D010085:Oxidative Phosphorylation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D021122:Protein Subunits / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome
chemical_list: D021122:Protein Subunits; D014157:Transcription Factors; D042967:Electron Transport Complex I