Alternative splicing is a key process in the control of mammalian gene expression and a major source of protein diversity. Errors in splicing regulation are implicated in many disease processes including cancer, but the cellular circuitry involved in this regulation is mostly unknown. Gene expression profiling using DNA microarrays has led to major advances in our understanding of gene regulatory systems on a genome wide scale. However, none of the commonly available systems of microarray analysis can detect changes in splicing and instead give information on the overall transcript abundance from each gene. These methods provide information on the first layer of gene regulation but miss many important changes in gene product caused by alterations in splicing pattern. The project proposed here will enable three groups to collaborate on establishing a new type of DNA microarray that allows the parallel analysis of multiple alternative splicing patterns. Each of the labs in this collaboration has unique expertise in the study of splicing. We will design and produce arrays of oligonucleotides that detect and measure splicing events in the mouse. This microarray method is well established for yeast splicing, and recent results demonstrate its ability to detect alternative splicing in more complex human cell lines and tissues. The proposal here is to apply it to specific systems of regulation in the mouse, including the nervous system and the heart. The goals of the project are to move the study of splicing regulation to the level of the whole genome, to comprehensively search for genes subject to specific splicing regulatory pathways, and to provide greater precision to gene expression profiling.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Resource-Related Research Projects (R24)
Project #
1R24GM070857-01
Application #
6758872
Study Section
Cell Development and Function Integrated Review Group (CDF)
Program Officer
Rhoades, Marcus M
Project Start
2004-04-01
Project End
2008-03-31
Budget Start
2004-04-01
Budget End
2005-03-31
Support Year
1
Fiscal Year
2004
Total Cost
$410,999
Indirect Cost
Name
University of California Los Angeles
Department
Microbiology/Immun/Virology
Type
Schools of Medicine
DUNS #
092530369
City
Los Angeles
State
CA
Country
United States
Zip Code
90095
Keppetipola, Niroshika; Sharma, Shalini; Li, Qin et al. (2012) Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2. Crit Rev Biochem Mol Biol 47:360-78
Chawla, Geetanjali; Lin, Chia-Ho; Han, Areum et al. (2009) Sam68 regulates a set of alternatively spliced exons during neurogenesis. Mol Cell Biol 29:201-13
Xing, Yi; Stoilov, Peter; Kapur, Karen et al. (2008) MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays. RNA 14:1470-9
Howell, Viive M; de Haan, Georgius; Bergren, Sarah et al. (2008) A targeted deleterious allele of the splicing factor SCNM1 in the mouse. Genetics 180:1419-27
Stoilov, Peter; Lin, Chia-Ho; Damoiseaux, Robert et al. (2008) A high-throughput screening strategy identifies cardiotonic steroids as alternative splicing modulators. Proc Natl Acad Sci U S A 105:11218-23
Boutz, Paul L; Stoilov, Peter; Li, Qin et al. (2007) A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons. Genes Dev 21:1636-52
Li, Qin; Lee, Ji-Ann; Black, Douglas L (2007) Neuronal regulation of alternative pre-mRNA splicing. Nat Rev Neurosci 8:819-31
Ni, Julie Z; Grate, Leslie; Donohue, John Paul et al. (2007) Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev 21:708-18
Srinivasan, Karpagam; Shiue, Lily; Hayes, Justin D et al. (2005) Detection and measurement of alternative splicing using splicing-sensitive microarrays. Methods 37:345-59
Xie, Jiuyong; Jan, Calvin; Stoilov, Peter et al. (2005) A consensus CaMK IV-responsive RNA sequence mediates regulation of alternative exons in neurons. RNA 11:1825-34