Description of the experiment (Rat)

There are more than 600 different skeletal muscles in the human body representing a complex and heterogeneous system capable of remodeling in response to mechanical load. Specific structure of fibers containing multiple nuclei make skeletal muscles very attractive, but a complicated case for studies aimed to explain the contribution of gene expression to the maintenance of homeostasis. Long-term muscle unloading which is observed in such conditions as bed rest, limb immobilization, or space flight, induces loss of muscle mass, strength, and function accompanied by muscle fiber transition from slow to fast phenotype [1] and leads to muscle atrophy [2].

On the other hand, activity and mechanical loading result in muscle hypertrophy and muscle growth and recovery. Prevention of muscle atrophy carries a clinical significance in the control of increased morbidity and mortality following physical inactivity and microgravity. On the molecular level, muscle atrophy is associated with strong changes in the interplay of protein synthesis and degradation with strong involvement of activity of a number of genes collectively referred as ‘atrogenes’ including members of ubiquitin-proteasome and the autophagy-lysosomal pathways [3]. While major transcriptional events associated with muscle atrophy-recovery processes are elucidated to some extent on gene level, little is known about involvement of non-coding regulatory elements. At the same time, utilization of different promoters of the same genes is one of the major sources of both production of alternative protein products and new deep insights of activity of transcription factors [4]. Moreover, recent advances in transcriptomics reveal a key role of promoter- and enhancer-associated RNAs in identification of cis-regulatory elements and control of gene expression [5].

Thus, in the current study, using cap analysis of gene expression (CAGE) we have created a whole-genome single nucleotide-level atlas of expression of transcription starting sites in the muscles of rats subjected to hindlimb unloading and subsequent recover to discover novel, still unidentified members of atrophy-recovery process and assess the contribution of regulatory elements to rearrangement of muscle fibers. We found that both slow-fast fiber transition and atrophy-recovery processes in muscles involve active differential promoters usage in the same genes.

Figure 1. Scheme of the experiment

Figure 2. Expression of TSS clusters across the samples