Alternative splicing landscape in mouse skeletal muscle and adipose tissue: Effects of intermittent fasting and exercise

Alternative splicing contributes to diversify the cellular protein landscape, but aberrant splicing is implicated in many diseases. To which extent mis-splicing contributes to insulin resistance as the causal defect of type 2 diabetes and whether this can be reversed by lifestyle interventions is largely unknown. Therefore, RNA sequencing data from skeletal muscle and adipose tissue of diabetes-susceptible NZO mice treated with or without intermittent fasting and of healthy C57BL/6J mice subjected to exercise were analyzed for alternative splicing differences using Whippet and rMATS. Diet and exercise interventions triggered comparable levels of splicing changes, although the splicing profile of skeletal muscle appeared to be more flexible than that of adipose tissue, with 72-114 differential splicing events in muscle and less than 25 in adipose tissue. Splicing changes induced by time-restricted feeding, alternate-day fasting and exercise were generally mild, with a maximal percent spliced in (PSI) difference of 67%, indicating that alternative splicing plays a rather minor role in lifestyle-induced adaptations of muscle and adipose tissue in mice. However, intron retention contributed to the regulation of gene expression, influencing genes whose expression was directly linked to phenotypic parameters (e.g. Eno2 and Pan2). Alternate-day fasting promoted skipping of exon 7 in Mlxipl (coding for ChREBP), thereby affecting the glucose sensing module of this carbohydrate-responsive transcription factor. Both intermittent fasting and exercise training led to alternative splicing of known diabetes-related GWAS genes (e.g. Abcc8, Ifnar2, Smarcad1), highlighting the potential metabolic relevance of these changes.