title: Transcriptional co-expression and co-regulation of genes coding for components of the oxidative phosphorylation system.
abstract: BACKGROUND
  The mitochondrial oxidative phosphorylation (OXPHOS) is critical for energy (ATP) production in eukaryotic cells. It was previously shown that genes coding for mitochondrial proteins involved in energy production co-express at the RNA level. Because the OXPHOS enzymes are multimeric complexes, we tested the hypothesis that genes coding for components of specific complexes are also co-regulated at the transcriptional level, and share common regulatory elements in their promoters.
  
  
  RESULTS
  We observed for the first time that, not only OXPHOS genes as a group co-express, but there is a co-expression of genes within each of the five OXPHOS enzyme complexes, showing a higher degree of complexity in gene co-regulation. In silico analysis of homologous promoter sequences in mammals identified the likely core promoter elements for most genes encoding OXPHOS subunits/assembly factors. The results included a significant abundance of previously identified sites (e.g. NRF1, NRF2, ERRA and YY1), as well as several sites that had not been previously detected. Although we identified patterns that correlated to OXPHOS gene expression, we did not detect an OXPHOS complex-specific arrangement of transcription factor binding sites within the core promoter that could explain the tight co-expression of these functionally related genes.
  
  
  CONCLUSIONS
  This study mapped the core promoters of most OXPHOS related genes and provided an example of gene expression regulation based on the final protein arrangement within a linear metabolic pathway.
authors.affiliation: Department of Cell Biology and Anatomy, University of Miami Miller School of Medicine, Miami, FL, USA. cvanwaveren@miamiproject.med.miami.edu
authors.forename: Corina
authors.initials: C
authors.lastname: van Waveren
authors.forename: Carlos T
authors.initials: CT
authors.lastname: Moraes
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D015971:Gene Expression Regulation, Enzymologic; D006801:Humans; D051379:Mice; D008928:Mitochondria / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D009097:Multienzyme Complexes / Q000235:genetics* / Q000378:metabolism*; D010085:Oxidative Phosphorylation; D011401:Promoter Regions, Genetic / Q000235:genetics; D021122:Protein Subunits / Q000235:genetics / Q000378:metabolism; D051381:Rats; D020218:Response Elements / Q000235:genetics; D012680:Sensitivity and Specificity; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D009097:Multienzyme Complexes; D021122:Protein Subunits; D014157:Transcription Factors