Thomas A Cooper, M.D.
S. Donald Greenberg Professor of Pathology
Department of Molecular and Cellular Biology
M.D.: Temple University Medical School, Philadelphia
Postdoctoral training: University of California, San Francisco
Alternative Splicing Regulation in Development and Disease
Up to seventy six percent of human genes express multiple mRNAs by alternative splicing of their pre-mRNAs. As a result, individual genes express multiple protein isoforms which can exhibit strikingly different functions. Alternative splicing is often regulated according to cell-specific patterns based on differentiated cell type, developmental stage, or in response to an external signal. Therefore, alternative splicing not only generates an extremely diverse human proteome from a relatively small number of genes but it also directs regulated expression of these proteins in response to a wide range of cues.
We are interested in understanding the mechanisms of splicing regulation, from how regulatory proteins tell the basal machinery whether to include or skip an exon to the signaling events that coordinate splicing changes during development.
We work on two families of splicing regulators (called CELF and MBNL proteins) which regulate splicing directly by binding to specific sequence motifs within pre-mRNAs. One question being addressed is, how does binding of a positive splicing regulator recruit or stabilize binding of the basal splicing machinery? Proteins that interact with the splicing regulators, either directly or by association in an activation complex, will be identified.
A large variety of splicing changes are developmentally regulated. Another goal is to determine how the activities of the splicing regulators are modified during development and to identify the signaling pathways responsible for their modification. We are also investigating the regulatory networks responsible for coordination of developmentally regulated splicing.
A separate area of investigation is the pathogenic mechanism of myotonic dystrophy (DM1), a dominantly inherited disease caused by an expanded CTG trinucleotide repeat in the 3' untranslated region of the DMPK gene. RNAs expressed from the expanded allele that contain long tracts of CUG repeats accumulate in the nucleus and disrupt alternative splicing. The mechanism is unknown but it involves disrupted functions of the CELF and MBNL proteins. We are using bioinformatic, biochemical, and molecular approaches to identify pre-mRNA targets of CELF and MBNL proteins whose mis-regulated splicing contributes to severe manifestations of disease. Transgenic mouse models that inducibly express CELF proteins or CUG repeat RNA are being used to investigate the mechanisms of pathogenesis and will be used to test treatment regimes.
- Kalsotra A and Cooper TA. Functional consequences of developmentally regulated alternative splicing Nature Rev. Genet. (In Press, Oct. 2011).
- Cooper TA. (2011). Regulating mRNA complexity in the mammalian brain. Nature Genetics 43, 618-619 (News and Views).
- Orengo JP, Ward AJ and Cooper TA. (2011) Alternative splicing misregulation secondary to skeletal muscle regeneration. Annals Neurology 69, 681-690.
- Kalsotra A, Wang K, Li PF and Cooper TA. (2010) MicroRNAs coordinate an alternative splicing network during mouse postnatal heart development. Genes Dev. 24, 653-658.
- Bland CS, Wang ET, Vu A, David MP, Castle JC, Johnson JM, Burge CB and Cooper TA. (2010). Global regulation of alternative splicing during myogenic differentiation. Nucl. Acids Res. 38, 7651-7654.
- Ward AJ, Rimer M, Killian JM, Dowling JJ, Cooper TA. (2010) CUGBP1 overexpression in mouse skeletal muscle reproduces features of myotonic dystrophy type 1. Hum Mol Genet. 19, 3614-3622.
- Wang GS, Kuyumcu-Martinez MN, Sarma S, Mathur N, Wehrens XH, Cooper TA. (2009) PKC inhibition ameliorates the cardiac phenotype in a mouse model of myotonic dystrophy type 1. J Clin Invest. 119, 3797-3806.
- Cooper TA. (2009) Neutralizing toxic RNA. Science 325, 272-327.
- Cooper TA, Wan L, and Dreyfuss G (2009). RNA and disease. Cell 136, 777–793.
- Kalsotra A, Tran D, Ward A, Xiao X, Burge CB, Castle JM, Johnson, JC, and Cooper TA (2008). A conserved program of regulated alternative splicing during vertebrate heart development. Proc. Nat’l Acad. Sci. 105, 20333-20338.