Description of the experiment (Human)

Skeletal muscle, as a very plastic tissue, is a unique object for studying the molecular mechanisms of adaptation to acute and chronic stressors (for example, to an increased level of physical activity). Using modern high-performance molecular biological methods (RNA sequencing in the modification of CAGE (cap analysis of gene expression) and high performance liquid chromatography in combination with tandem mass spectrometry) and bioinformatic approaches, we have investigated the mechanisms of regulation of gene and protein expression during adaptation of human skeletal muscle to aerobic exercise.

Using the CAGE method, more than 30,000 transcription initiation sites were identified and annotated on genes; a complete resource (database) of transcription starts for human skeletal muscle has been created. Of all genes expressed in muscle (~ 12,000), about two thirds have more than one CAGE start. Apparently, the function of alternative starts in a gene is associated not only (not so much) with the generation of alternative protein isoforms, but with fine regulation of the expression of one mRNA isoform due to the activation of various alternative starts by transcription factors specific to them. When studying the response of human skeletal muscle to a single physical exercise, we managed to show that alternative starts of transcription make a significant contribution (10%) to the change in gene expression in response to exercise. Using data on open chromatin and on the density of transcription factors binding sites surrounding each start, the coordinates of the promoter regions for all genes expressed in human skeletal muscle were determined. These data made it possible to identify transcription factors involved in the regulation of gene expression in various clusters of co-expressed (co-regulated) genes. The approach developed by us can be used to study the regulation of gene expression in human skeletal muscles under various influences. When studying the effects of regular exposure (two months of regular aerobic exercise), it was found that the pattern of regulation of the content of highly represented proteins depends on the functions of proteins: the content of proteins associated with the extracellular matrix is regulated at the level of mRNA, while the content of mitochondrial proteins is not. The latter is an extremely interesting observation, since the activation of mitochondrial biogenesis (and an increase in muscle performance) is the most striking change in muscle phenotype that occurs with regular aerobic exercise. Bioinformatic analysis of the data allowed us to suggest that an increase in the content of some muscle proteins (including mitochondrial proteins) is associated with an increase in their stability through a chaperone-dependent mechanism and / or with a decrease in the rate of their degradation.

The data obtained expand our understanding of the fundamental mechanisms underlying the regulation of gene expression and protein content in human skeletal muscle under single and regular stress exposure. Elucidation of these mechanisms can become the basis for the selection of specific physiological and / or pharmacological approaches that purposefully affect the content of specific proteins (for example, proteins associated with the extracellular matrix, mitochondrial proteins) in skeletal muscles.