Alternative usage of dominating TSS

We found that promoter switches play a substantial role in gene expression associated with atrophy processes in both types of muscles. For example, on the first day of recovery (R1 phase) the dominating (i.e. the most transcribed) TSS of Myh4 gene was changed to the start of full-length isoform while the isoforms expressed in control samples were supposedly heavily 5’-truncated (Figure 4A).

Figure 4. Alternative TSS in genes Myh4 (A) and Rtkn (B) shown in GTRD web browser. See SF4 for the full figure

In total, 24 genes upregulated in slow muscle on the first day of recovery had their dominating TSS changed (See ST8) including Dcn which promotes muscle regeneration [3] Ggnbp2 which regulates trophoblast proliferation [4] , Glul which is involved in the regulation of glycogen synthesis via the up-regulation of glycogen synthase [5], Limch1 which is unregulated as a result of endurance exercise in glycogen deficient mouse model [6] , Pld3 which supposedly plays a role in myotube formation [7]. Interestingly, only 3 of those 24 genes were also upregulated and had their dominating TSS changed on the first day of recovery in fast muscle - Bcurl, Syncrip and Zmynd8.

Similarly, 28 genes were both upregulated and changed their dominating TSS in fast muscle on the first day of recovery, including Ampd3 - a subunit of AMP deaminase [8], Ankh - a mediator of cellular export of ATP, Dapk2, which is phosphorylated in Ca2+ independent manner by AMPK in muscle tissue, undergoing dystrophy [9] , Flt1 - a VEGF receptor, essential for skeletal muscle function [10], Lpin1 which is essential for lipid metabolism and ATP synthesis [11], Macf1, which maintains cellular components of microtubules in muscle [12] , Myl12a - myosin regulatory subunit, Prkag2, which mutations are associated with skeletal muscle glycogenosis [13] , Xirp1 - a marker of wounded skeletal muscle [14].