A functionally integrated cross-tissue alternative splicing program during short-term calorie restriction

Alternative splicing (AS) involves production of several different RNA molecules from a single pre-mRNA. Calorie restriction (CR) is a sustained calorie deficit without malnutrition, which extends health and lifespan. AS is dysregulated in aging but less so following CR, suggesting a role for AS in the beneficial effects of CR. To test the hypothesis that AS is involved in the CR response and explore its tissue specificity, male C57BL/6 mice were exposed to 3 months of graded CR (0-40% at 10% increments) and RNA sequencing data from six tissues (epididymal white adipose tissue [eWAT], liver, hypothalamus, gastrocnemius muscle, testes, and stomach) were analyzed to provide a multi-tissue characterization of differential AS (DAS). The number of differentially expressed splicing regulators increased with CR levels in all tissues but primarily the muscle, eWAT, and liver. The total number of DAS genes also increased with increasing CR levels and was largely tissue-specific. Most DAS genes were not differentially expressed. DAS was functionally integrated across tissues with the same processes being overrepresented: namely, mitochondria and oxidative phosphorylation, transcription and translation, and quality checking and degradation of RNA and especially proteins. This study demonstrates that short-term CR evokes a functionally integrated cross-tissue AS response in mice that is largely independent of expression changes.