Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions

Brinegar, Amy E.; Xia, Zheng; Loehr, James A.; Li, Wei; Rodney, George G.; Cooper, Thomas A.

doi:10.1101/124230

Cited by 24 publications

(40 citation statements)

References 61 publications

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“…Well-studied examples in the nervous system include AS regulation by NOVA2 which impacts a gene network whose protein products function at neuronal synapses (Ule et al, 2005); AS regulation by RBFOX which impacts genes whose proteins localize to the axon initial segment (Jacko et al, 2018); and AS regulation by PTBP2 in the embryonic brain which is important to prevent premature neurogenesis and maintain neuronal precursors (Licatalosi et al, 2012). Similarly, regulation of AS by tissue-restricted RBPs has critical roles in development of the heart, skeletal muscle, liver, and skin (Bangru et al, 2018;Giudice et al, 2014;Bhate et al, 2015;Brinegar et al, 2017;Dittmar et al, 2012). In contrast, much less is known about the regulation and functional roles of AS in spermatogenesis, despite the long-standing recognition that unusually high levels of AS isoforms are expressed in the testis compared to other tissues (Yeo et al, 2004;Clark et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

“…Splicing of Ppp3ca exon 13 is regulated in a tissue-specific manner and increases during postnatal development of skeletal muscle. Furthermore, functional studies in muscle indicate that AS of exon 13 impacts the intrinsic phosphatase activity of calcineurin, with reduced activity for polypeptides encoded by mRNA that contain exon 13 (Brinegar et al, 2017). Inclusion of Ppp3ca exon 13 is higher in spermatocytes compared to spermatogonia, and is abnormally elevated in Ptbp2 cKO versus WT testes ( Figure 5A).…”

Section: Ptbp2 Post-transcriptionally Controls Expression Of Mitochonmentioning

confidence: 99%

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PTBP2-dependent alternative splicing regulates protein transport and mitochondria morphology in post-meiotic germ cells.

Hannigan

Fujioka

Brett-Morris

et al. 2018

Preprint

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The RNA binding protein PTBP2 (polypyrimidine tract binding protein 2) is a key regulator of tissue-specific alternative RNA splicing. In the testis, PTBP2 is expressed in meiotic and post-meiotic germ cells (spermatocytes and spermatids, respectively). In these cells, PTBP2 is required for proper alternative mRNA splicing for over 200 genes, disproportionately affecting genes encoding proteins involved in protein trafficking via transport vesicles. In this study, we used electron microscopy to test the hypothesis that protein trafficking is impaired in the absence of PTBP2, and to further investigate why spermatogenesis abruptly ceases in PTBP2-deficienct spermatids. Ultrastructural analysis shows that protein trafficking in spermatids is aberrant in the absence of PTBP2. Unexpectedly, we also found that mitochondria morphology and number are significantly altered in PTBP2-deficient spermatids, consistent with increased mitochondria fission. Furthermore, we show that genes with key roles in mitochondria dynamics and function are post-transcriptionally regulated by PTBP2 and in different stages of spermatogenesis. Collectively, the data provide ultrastructural evidence that alternative splicing regulation by PTBP2 during spermatogenesis is critical for proper regulation of protein trafficking and mitochondria morphology.

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Section: Discussionmentioning

confidence: 99%

Section: Ptbp2 Post-transcriptionally Controls Expression Of Mitochonmentioning

confidence: 99%

PTBP2-dependent alternative splicing regulates protein transport and mitochondria morphology in post-meiotic germ cells.

Hannigan

Fujioka

Brett-Morris

et al. 2018

Preprint

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“…Skeletal muscle undergoes extensive physiological changes during development to produce fully functional adult muscles [45]. At the molecular level, these changes are accompanied by numerous transcriptional and posttranscriptional changes, including those controlled by alternative splicing mechanisms [46,47]. Alternative splicing changes are controlled mostly by RNA-binding proteins (RBPs) that change their expression levels during development.…”

Section: Alternative Splicing In Skeletal Musclementioning

confidence: 99%

RNA processing in skeletal muscle biology and disease

2019

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RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle. Furthermore, misregulation of RNA processing is implicated in muscle diseases. In this review, we comprehensively summarize recent studies in skeletal muscle that demonstrated: (i) the importance of RNA processing, (ii) the RNA-binding proteins that are involved, and (iii) diseases associated with defects in RNA processing. ARTICLE HISTORY

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“…While the top two clusters were related to DNA binding and transcriptional regulation and included known targets such as E2f5 [39], Pax3 [40], and Sox9 [41], both the third and fifth clusters included genes related to RNA metabolism. Since regulated splicing plays a central role in promoting myogenesis [4,6,7], we investigated whether miR-1/206 control muscle differentiation by specifically targeting RNA processing factors.…”

Section: Resultsmentioning

confidence: 99%

“…A complex network of integrated transcriptional and post-transcriptional regulatory mechanisms control skeletal muscle gene expression. Overall, skeletal muscle displays one of the most tissue-specific splicing profiles, and changes in alternative splicing trigger proper temporal gene expression patterns during myogenesis [1–7]. Moreover, biochemical and biophysical properties of many components of the contractile machinery can be fine-tuned by selectively expressing specialized isoforms.…”

Section: Introductionmentioning

confidence: 99%

miR-1/206 down-regulates splicing factor Srsf9 to promote myogenesis

Bjorkman

Buvoli

Pugach

et al. 2019

Preprint

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BackgroundMyogenesis is driven by specific changes in the transcriptome that occur during the different stages of muscle differentiation. In addition to controlled transcriptional transitions, several other post-transcriptional mechanisms direct muscle differentiation. Both alternative splicing and miRNA activity regulate gene expression and production of specialized protein isoforms. Importantly, disruption of either process often results in severe phenotypes as reported for several muscle diseases. Thus, broadening our understanding of the post-transcriptional pathways that operate in muscles will lay the foundation for future therapeutic interventions.MethodsWe employed bioinformatics analysis in concert with the well-established C2C12 cell system for predicting and validating novel miR-1 and miR-206 targets engaged in muscle differentiation. We used reporter gene assays to test direct miRNA targeting and studied C2C12 cells stably expressing one of the cDNA candidates fused to a heterologous, miRNA-resistant 3’ UTR. We monitored effects on differentiation by measuring fusion index, myotube area, and myogenic gene expression during time course differentiation experiments.ResultsGene ontology analysis revealed a strongly enriched set of putative miR-1 and miR-206 targets associated with RNA metabolism. Notably, the expression levels of several candidates decreased during C2C12 differentiation. We discovered that the splicing factor Srsf9 is a direct target of both miRNAs during myogenesis. Persistent Srsf9 expression during differentiation impaired myotube formation and blunted induction of the early pro-differentiation factor myogenin as well as the late differentiation marker sarcomeric myosin, Myh8.ConclusionsOur data uncover novel miR-1 and miR-206 cellular targets and establish a functional link between the splicing factor Srsf9 and myoblast differentiation. The finding that miRNA-mediated clearance of Srsf9 is a key myogenic event illustrates the coordinated and sophisticated interplay between the diverse components of the gene regulatory network.

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Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions

Cited by 24 publications

References 61 publications

PTBP2-dependent alternative splicing regulates protein transport and mitochondria morphology in post-meiotic germ cells.

PTBP2-dependent alternative splicing regulates protein transport and mitochondria morphology in post-meiotic germ cells.

RNA processing in skeletal muscle biology and disease

miR-1/206 down-regulates splicing factor Srsf9 to promote myogenesis

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