PURPOSE: The purpose of this study was to define the relationship between muscle mechanical conditions and gene expression in rat skeletal muscle by varying stress and contraction mode. Eccentric and isometric contractions at different frequencies were used to independently vary mechanical stress (force/PCSA) from contraction mode (eccentric vs. isometric). The goal was to determine whether muscle tissue simply responds to mechanical stress, contraction mode, or a combination of the two. METHODS: The experimental model used was stimulation of the rat dorsiflexors in vivo, via a peroneal nerve cuff electrode (n=25), activating them at high or low frequencies (150 Hz or 40 Hz) either eccentrically or isometric ally. This experimental design yielded four experimental groups. Eccentric contractions were induced by forced plantarflexion of the ankle. Muscle physiological, immunohistochemical and gene expression changes were then measured 24 hours after the exercise bout. Gene expression was measured for each muscle using quantitative PCR. Specific primer pairs were designed to amplify myostatin, MyoD, myogenin, MLP (also referred to as CRP3), CARP, Arpp/Ankrd2 and embryonic MHC. RESULTS: Peak stress was the best predictor of muscle injury, independent of contraction mode (i.e., eccentric or isometric),. When peak stresses were matched, no physiologic or immunohistochemical differences were detected between isometric and eccentric contractions. This indicated that structurally and physiologically, stress affected the muscle independent of mode. In contrast, the expression of certain myogenic regulatory and MARP genes (myoD, myogenin, MLP, and CARP) depended both on peak muscle stress achieved during contraction and contraction mode while Arpp/Ankrd2 was dramatically upregulated only by eccentric contractions, but not by isometric contractions. Conclusions: These data demonstrate that, structurally and physiologically, the stress imposed upon a muscle determines the magnitude of injury, represented either by peak tetanic tension or altered immunohistochemical staining. In contrast, several muscle-specific genes (myoD, myogenin, MLP, and CARP) were sensitive both to muscle contractile stress and contraction mode while another (Arpp/Ankrd2) was sensitive only to contraction mode. The gene expression results thus indicate biological sensitivity that is not apparent at the functional level. The data also suggest that the Arpp/Ankrd2 gene may be a sensor of eccentric contractions.