Ribosome production is an early event during skeletal muscle hypertrophy and precedes muscle protein accretion. Signaling via mTOR is crucial for ribosome production and hypertrophy, however the mechanisms by which it regulates these processes remain to be identified. Herein, we investigated the activation of mTOR signaling in hypertrophying myotubes, and determined that mTOR coordinates various aspects of gene expression important for ribosome production. First, inhibition of translation with cycloheximide had a more potent effect on protein synthesis than Rapamycin indicating that mTOR function during hypertrophy is not on general, but rather specific protein synthesis. Second, blocking Pol II transcription had a similar effect as Rapamycin and unexpectedly, revealed the necessity of Pol II transcription for Pol I transcription, suggesting that mTOR may regulate ribosome production also by controlling Class II genes at the transcription level. Third, Pol I activity is essential for rDNA transcription, and surprisingly, for protein synthesis as selective Pol I inhibition blunted rDNA transcription, protein synthesis and the hypertrophic response of myotubes. Finally, mTOR has nuclear localization in muscle, which is not sensitive to Rapamycin. Inhibition of mTOR signaling by Rapamycin disrupted mTOR-rDNA promoter interaction, and resulted in altered histone marks indicative of repressed transcription and formation of higher order chromatin structure. Thus mTOR signaling appears to regulate muscle hypertrophy by affecting protein synthesis, Class I and II gene expression and chromatin remodeling.