BioProject

A majority of genes code for non-protein-coding RNA (ncRNA). Only a handful of ncRNA have characterised molecular functions, including key epigenetic roles in development and human disease. In human skeletal muscle reliance on suboptimal sequencing-based data has obfuscated characterization of ncRNAs. Herein, using more comprehensive RNA profiling and data-driven quantitative network methods we study regulation of ncRNAs during skeletal muscle hypertrophy. Across five independent supervised exercise-training studies (n=144), 61% of individuals accrued muscle mass beyond established technical variation (lean mass responders, LMR) with the remainder show no measurable lean mass response (NMLMR). The LMR group alone demonstrated differential expression (DE) of 50 ncRNA genes (FDR <1%) and further modelling identified a total of 110 ncRNAs of potential interest. Critically, expression of these ncRNAs was indistinguishable between LMR vs NMLMR at baseline. Notably, <5% of these candidate ncRNAs were detected as being regulated by exercise training using sequencing. A robust co-expression model of the human muscle transcriptome (n=437) used to assign each ncRNA to functional pathways or single-cell types. Candidates, such as the hypertrophy-related ncRNA CYTOR, was leukocyte associated (FDR = 4.9 x10-7; FE = 6.6) and highly expressed in immune-related cells. PPP1CB-DT co-expressed with myofibril assembly genes (FDR = 8.2 x10-8; FE = 47.5), positively associating with type II fibre markers (e.g., TNNT3: r =0.37; FDR = 2.57 x10-14), while others (e.g. EEF1A1P24 and TMSB4XP8) co-expressed angiogenesis pathways. MYREM was positively associated with hypertrophy and we established it has a distinct myonuclear expression in vivo, using merfish probes. We show that single-cell type associations are readily identifiable from bulk transcriptomic data, and that hypertrophy-linked ncRNA genes appear to mediate their association with muscle growth via multiple cell types. A total of 144 paired sample comparisons were made for the continous (change in lean mass) versus change in gene expression analysis using 137 paris of samples. 7 baseline samples from the HALL study represent a single baseline biopsy and thereafter each leg was subject to a distinct RT protocol with an individual measure of lean mass before and lean mass afterwards from the same leg. Overall design: Samples marked RT_Study were used the analysis of muscle before and after supervised exercise training (resistance exercise in this case).