In addition to transcriptional regulation of gene output, mammalian genomes produce extensive transcriptome and proteome diversity by alternative splicing and selection of alternative 3'mRNA ends during pre-mRNA processing. As for transcription, transcriptome processing is extensively regulated in response to dynamic physiological needs. The regulation of transcriptome processing involves interconnected networks controlled by RNA binding proteins that bind to preferred sequence motifs within the pre-mRNA near the sites of regulated processing. The long term goal of this project is to determine the extent, regulatory mechanisms, and functional consequences of transcriptome processing in adult skeletal muscle. The disruption of transcriptome processing networks contributes to disease in skeletal muscle yet little is known regarding the extent or functions of normal regulation. In the first part of this proposal, we will identify the regulatory networks controlled by the Fox family of RNA binding proteins in skeletal muscle and determine their functions during myoblast differentiation. We will use tissue specific and inducible knock outs of the two Fox genes expressed in skeletal muscle to determine the functions of the regulatory networks in myofibers and satellite cells in adult skeletal muscle. In the second part of the proposal, we will identify additional regulatory networks operative during myoblast differentiation using a bichromatic splicing reporter in high throughput RNAi screens. Knowledge gained will be directed toward understanding the roles of these networks in adult skeletal muscle. The results will provide a new understanding of the role of nuclear post-transcriptional regulation in the diverse homeostatic functions of adult skeletal muscle and its capacity for repair. This understanding is important for development and application of novel therapeutic strategies to conditions that negatively affect skeletal muscle function.

Public Health Relevance

Post-transcriptional regulation of gene expression, such as alternative splicing and 3'end processing, play a large role in controlling gene expression. This proposal studies the mechanisms of alternative splicing and 3'end processing during skeletal muscle differentiation and in adult skeletal muscle tissue. This information will be used to understand normal processes in skeletal muscle useful for future development of therapeutic approaches to reverse or circumvent disease.

National Institute of Health (NIH)
National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-MOSS-K (02))
Program Officer
Boyce, Amanda T
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Baylor College of Medicine
Schools of Medicine
United States
Zip Code
Blue, R Eric; Koushik, Amrita; Engels, Nichlas M et al. (2018) Modulation of alternative splicing of trafficking genes by genome editing reveals functional consequences in muscle biology. Int J Biochem Cell Biol 105:134-143
Morriss, Ginny R; Rajapakshe, Kimal; Huang, Shixia et al. (2018) Mechanisms of skeletal muscle wasting in a mouse model for myotonic dystrophy type 1. Hum Mol Genet 27:2789-2804
Singh, Ravi K; Kolonin, Arseniy M; Fiorotto, Marta L et al. (2018) Rbfox-Splicing Factors Maintain Skeletal Muscle Mass by Regulating Calpain3 and Proteostasis. Cell Rep 24:197-208
Brinegar, Amy E; Xia, Zheng; Loehr, James Anthony et al. (2017) Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions. Elife 6:
Manning, Kassie S; Rao, Ashish N; Castro, Miguel et al. (2017) BNANC Gapmers Revert Splicing and Reduce RNA Foci with Low Toxicity in Myotonic Dystrophy Cells. ACS Chem Biol 12:2503-2509
Sharpe, Joshua J; Cooper, Thomas A (2017) Unexpected consequences: exon skipping caused by CRISPR-generated mutations. Genome Biol 18:109
Morriss, Ginny R; Cooper, Thomas A (2017) Protein sequestration as a normal function of long noncoding RNAs and a pathogenic mechanism of RNAs containing nucleotide repeat expansions. Hum Genet 136:1247-1263
Manning, Kassie S; Cooper, Thomas A (2017) The roles of RNA processing in translating genotype to phenotype. Nat Rev Mol Cell Biol 18:102-114
Cox, Diana C; Cooper, Thomas A (2016) Non-canonical RAN Translation of CGG Repeats Has Canonical Requirements. Mol Cell 62:155-156
Giudice, Jimena; Loehr, James A; Rodney, George G et al. (2016) Alternative Splicing of Four Trafficking Genes Regulates Myofiber Structure and Skeletal Muscle Physiology. Cell Rep 17:1923-1933

Showing the most recent 10 out of 36 publications