Global alternative splicing landscape of skeletal muscle atrophy induced by hindlimb unloading

Abstract

Background: Long-term exposure to microgravity will cause skeletal muscle atrophy, which can cause serious harm to astronauts in space travel. Therefore, it is important to explore skeletal muscle atrophy's molecular mechanism for its prevention and treatment. However, as an important regulatory approach of skeletal muscle physiology, the role of alternative splicing in skeletal muscle atrophy, especially skeletal muscle atrophy caused by disuse, is unclear.Methods: We established a rat hindlimb unloading model and performed RNA sequencing on soleus muscle, which was seriously atrophied during unloading. Several bioinformatics methods were used to identify alternative splicing events and determine their gene functions.Results: Many alternative splicing events were found to occur at different time points (12 h, 24 h, 36 h, 3 days, and 7 days) after hindlimb unloading. These differential alternative splicing events mainly occurred in the gene's coding domain sequence region, and 59% of the alternative splicing events caused open reading frameshift. Bioinformatics analysis results showed that genes with different alternative splicing events were enriched in multiple pathways related to muscle atrophy, including the insulin signaling pathway, endocytosis, mitophagy, and ubiquitin-proteasome pathway. Moreover, alternative splicing of several deubiquitinase genes persisted during skeletal muscle atrophy induced by unloading. Additionally, we identified 10 differentially expressed RNA binding proteins during skeletal muscle atrophy induced by unloading, mainly containing Xpo4, Eif4e2, P4ha1, Lrrfip1, Zc3h14, Emg1, Hnrnp h1, Mbnl2, RBfox1, and Mbnl1. Hnrnp h1 and Mbnl2 were significantly downregulated, and RBfox1 and Mbnl1 were significantly upregulated during skeletal muscle atrophy caused by unloading.Conclusions: To the best of our knowledge, the present study is the first to propose alternative splicing alterations related to disuse-induced muscle atrophy, emphasizing that alternative splicing is a new focus of attention in the occurrence of muscle atrophy.

Muscle fibre transition and transcriptional changes of horse skeletal muscles during traditional Mongolian endurance training

“…Alternative splicing events that play a role in skeletal muscle have been reported regulating myogenesis, 53–55 muscle contraction, 56,57 and muscle atrophy 58–60 . In our study, the DAS events during training were investigated.…”

“…50 The higher levels of Map1lc3a (Lc3a), Map1lc3b (Lc3b) and Bnip3 were also observed Alternative splicing events that play a role in skeletal muscle have been reported regulating myogenesis, [53][54][55] muscle contraction, 56,57 and muscle atrophy. [58][59][60] In our study, the DAS events during training were investigated. A great number of alternative splicing events happened in Ttn, including three DAS events.…”

Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflight

“…Protein degradation via the ubiquitin-proteasome pathway is a major cause of acute muscle atrophy, which represents muscle loss that occurs within approximately 48 h of an atrophy-inducing perturbation [ 57 ]. Acute activation of the ubiquitin-proteasome pathway has been shown to be directed by DGE [ 58 ]; however, a recent study in rats [ 39 ] discovered DAS of ubiquitin-proteasome pathway transcripts after 7 days of hindlimb unloading. Following 9 weeks of microgravity exposure, we observed DAS, but not DGE, of transcripts encoding ubiquitin-proteasome pathway proteins in both the gastrocnemius (two DAS events; see Table 2 ) and the quadriceps (four DAS events; see Table 3 ).…”

“…In fact, approximately 95% of human genes have been found to exhibit alternatively spliced isoforms [ 24 ], most attributable to the best characterized and most prevalent AS types: skipped exon (SE) and mutually exclusive exon (MXE) events [ 25 ]. The role of AS in skeletal muscle on Earth has been well-annotated, including regulation of myogenesis [ 26 – 28 ], cell type-specific function [ 29 – 31 ], fiber-type-specific function [ 32 ], muscle contraction [ 33 , 34 ], calcium handling [ 35 – 37 ], muscle atrophy [ 38 , 39 ], and muscular dystrophy [ 40 ]. However, there have been no investigations of differential alternative splicing (DAS) in skeletal muscle during or following spaceflight.…”