Transcriptional response of human cells to the absence of mitochondrial DNA

Mitochondrial biogenesis is under the control of two different genetic systems: the nuclear genome (nDNA) and the mitochondrial genome (mtDNA). mtDNA is a circular genome of 16.6 kb encoding 13 of the approximately 90 subunits that form the respiratory chain, the remaining ones being encoded by the nuclear genome (nDNA). Eukaryotic cells are able to monitor and respond to changes in mitochondrial function through alterations in nuclear gene expression, a phenomenon first defined in yeast and known as retrograde regulation. With this experiment we aimed to identify the set of nuclear genes that significantly change their expression level in response to depletion of mtDNA. Keywords: case-control We used Affymetrix HG-U133A GeneChips to study the transcriptome of two human cell lines, 143BTK- and A549, which had been entirely depleted of mtDNA (rho0 cells), and compared it with the corresponding undepleted parental cells (rho+ cells). Three independent biological replicates were analyzed for each cell line and treatment group.