["The Journal of Physiology, EarlyView. ", "\nAbstract figure legend Disuse, like several other pathological conditions, has specific effects on various skeletal muscles. The mechanisms underlying these responses remain unclear. Three‐week bed rest resulted in a greater decrease in lean mass, endurance and more pronounced changes in the proteome and transcriptome of the calf muscles than the thigh muscles. A greater decrease in calf muscle mass was associated with suppression of translation regulators. Meanwhile, a decrease in endurance of the calf muscles was associated with mitochondrial dysregulation. Most large‐scale changes in the transcriptome did not translate into changes in the proteome. However, changes in the RNA levels played a dominant role in regulating expression of specific proteins, such as mitochondrial biogenesis regulators, whereas for others (proteins of ribosome and exosome, etc.) this factor played little or no role.\n\n\n\n\n\n\n\n\n\nAbstract\nDisuse, like several other pathological conditions, has specific effects on various skeletal muscles; the mechanisms underlying these responses remain unclear. We aimed to compare the disuse‐induced changes in the phenotype and proteome of the calf and thigh muscles, and to assess the extent to which these proteomic changes are regulated at the mRNA and other levels. Twelve healthy young males participated in a 3‐week bed rest. Disuse resulted in a greater decrease in lean mass, aerobic performance, and changes in the proteome and transcriptome of the calf muscles (m. soleus) than the thigh muscles (m. vastus lateralis). A greater decrease in calf muscle mass was associated with a decrease in the expression/deactivation of translation regulators, but not with the expression of the main sarcomeric proteins. At the same time, a significant decrease in aerobic performance of the ankle plantar flexors occurred without changing the expression of oxidative enzymes – a marker of mitochondrial density. That decrease was associated with dysregulation of mitochondrial biogenesis. Most large‐scale changes in the transcriptome did not translate into changes in the proteome, indicating post‐transcription protein buffering. However, changes in the RNA levels were revealed to play a dominant role in regulating specific proteins, whereas for others, this factor played little or no role. In conclusion, our findings partially explain why calf muscles with a strong postural function are more sensitive to short‐term disuse. This provides a foundation for developing targeted approaches to counteract the negative effects of disuse on different muscles.\n\n\n\n\n\n\n\n\n\nKey points\n\nDisuse, like several other pathological conditions, has specific effects on various skeletal muscles. The mechanisms underlying these responses remain unclear.\nThree‐week bed rest resulted in a greater decrease in lean mass, endurance, and more pronounced changes in the proteome and transcriptome of the calf muscles than the thigh muscles.\nA greater decrease in calf muscle mass was associated with suppression of translation regulators. Meanwhile, a decrease in endurance of the calf muscles was associated with mitochondrial dysregulation.\nMost large‐scale changes in the transcriptome did not translate into changes in the proteome. However, changes in the RNA levels played a dominant role in regulating expression of specific proteins, such as mitochondrial biogenesis regulators, whereas for others (proteins of ribosome and exosome, etc.) this factor played little or no role.\nOur findings provide a foundation for developing targeted approaches to counteract the negative effects of disuse on different muscles.\n\n\n"]