E-GEOD-5332 - Transcription profiling of mouse TSC2-/- embryonic fibroblasts: vehicle-treated, rapamycin-treated, gfp-infected, and pgc-1alpha-infected samples reveals the mTOR pathway controls mitochondrial gene expression and respiration through the YY1/PGC-1alpha transcriptional complex

Submitted on 18 July 2006, released on 13 June 2008, last updated on 27 March 2012
Mus musculus
Samples (12)
Array (1)
Protocols (9)
Mitochondrial oxidative function is tightly controlled to maintain energy homeostasis in response to nutrient and hormonal signals. An important cellular component in the energy sensing response is the target of rapamycin (TOR) kinase pathway; however whether and how mTOR controls mitochondrial oxidative activity is unknown. Here, we show that mTOR kinase activity stimulates mitochondrial gene expression and oxidative function. In skeletal muscle cells and TSC2-/- MEFs, the mTOR inhibitor rapamycin largely decreased gene expression of mitochondrial transcriptional regulators such as PGC-1alpha and the transcription factors ERRalpha and NRFs. As a consequence, mitochondrial gene expression and oxygen consumption were reduced upon mTOR inhibition. Using computational genomics, we identified the transcription factor YY1 as a common target of mTOR and PGC-1alpha that controls mitochondrial gene expression. Inhibition of mTOR resulted in a failure of YY1 to interact and be coactivated by PGC-1alpha. Notably, knock-down of YY1 in skeletal muscle cells caused a significant decrease in mRNAs of mitochondrial regulators and mitochondrial genes that resulted in a decrease in respiration. Moreover, YY1 was required for rapamycin-dependent repression of mitochondrial genes. Thus, we have identified a novel mechanism in which a nutrient sensor (mTOR) balances energy metabolism via transcriptional control of mitochondrial oxidative function. These results have important implications for our understanding of how these pathways might be altered in metabolic diseases and cancer. Experiment Overall Design: Using Affymetrix MOE430 v2 gene chips, biological triplicates of each condition were analyzed: vehicle-treated, rapamycin-treated, gfp-infected, and pgc-1alpha-infected resulting in a total of 12 samples. Experiment Overall Design: Data were analyzed by RMA (with default settings) in BioConductor 1.2 -- one batch for the Rapamycin vs. Vehicle, and another batch for the PGC vs GFP.
Experiment types
transcription profiling by array, unknown experiment type
mTOR controls mitochondrial oxidative function through a YY1-PGC-1alpha transcriptional complex. John T Cunningham, Joseph T Rodgers, Daniel H Arlow, Francisca Vazquez, Vamsi K Mootha, Pere Puigserver. Nature 450(7170):736-40 (2007)
Investigation descriptionE-GEOD-5332.idf.txt
Sample and data relationshipE-GEOD-5332.sdrf.txt
Raw data (1)E-GEOD-5332.raw.1.zip
Processed data (1)E-GEOD-5332.processed.1.zip
Array designA-AFFY-45.adf.txt
R ExpressionSetE-GEOD-5332.eSet.r