Intricate gene regulatory networks direct the development of multi-cellular eukaryotes. Although transcription regulation is the best understood mechanism by which these networks are controlled, it has recently become clear that alternative splicing is an equally important regulatory mechanism. Despite the fact that the majority of eukaryotic genes encode pre-mRNAs that are alternatively spliced (at least 65% of human genes), very few splicing regulatory factors have been identified, and the target genes that are controlled by specific splicing regulators are largely unknown. Alternative splicing is primarily thought to be regulated by auxiliary splicing factors - proteins that are not core components of the spliceosome. Auxiliary splicing factors function by binding to the pre-mRNA where they modulate the association of the spliceosome with the regulated splice sites. Recent work from our group and others, however, suggests that components of the general splicing machinery may also play important roles in regulating alternative splicing. This may in part account for the apparent discrepancy between the numbers of known splicing regulators and regulatory targets. The goals of this research proposal are to identify proteins that regulate alternative splicing and their regulatory targets on a genome-wide level, and to determine the biochemical mechanisms by which these proteins regulate alternative splicing using Drosophila melaongaster as a model system. We will first perform microarray experiments to identify alternatively spliced exons that are regulated by the entire complement of RNA binding proteins encoded by the Drosophila genome and to build a model of the splicing regulatory networks in Drosophila. These experiments will be complemented by a combination of biochemical, genetic, genomic, and bioinformatics experiments designed to determine the mechanisms by which both auxiliary and general splicing factors function to control alternative splicing. Together these experiments will provide tremendous insight into the mechanisms of alternative splicing. Given that the proteins involved in regulating alternative splicing in Drosophila and humans are similar, that a number of human diseases are caused by defects in the normal patterns of alternative splicing, and that the human homologs of many of the proteins we will be studying have been implicated in human diseases, it is likely that the discoveries we make will be of direct relevance to human health. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM062516-07
Application #
7267045
Study Section
Molecular Genetics C Study Section (MGC)
Program Officer
Rhoades, Marcus M
Project Start
2001-03-01
Project End
2010-07-31
Budget Start
2007-08-01
Budget End
2008-07-31
Support Year
7
Fiscal Year
2007
Total Cost
$339,387
Indirect Cost
Name
University of Connecticut
Department
Genetics
Type
Schools of Medicine
DUNS #
022254226
City
Farmington
State
CT
Country
United States
Zip Code
06030
Eipper-Mains, J E; Kiraly, D D; Duff, M O et al. (2013) Effects of cocaine and withdrawal on the mouse nucleus accumbens transcriptome. Genes Brain Behav 12:21-33
Eipper-Mains, Jodi E; Eipper, Betty A; Mains, Richard E (2012) Global Approaches to the Role of miRNAs in Drug-Induced Changes in Gene Expression. Front Genet 3:109
Hale, Caryn R; Majumdar, Sonali; Elmore, Joshua et al. (2012) Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol Cell 45:292-302
Eipper-Mains, Jodi E; Kiraly, Drew D; Palakodeti, Dasaradhi et al. (2011) microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs. RNA 17:1529-43
McManus, C Joel; Graveley, Brenton R (2011) RNA structure and the mechanisms of alternative splicing. Curr Opin Genet Dev 21:373-9
Brooks, Angela N; Yang, Li; Duff, Michael O et al. (2011) Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res 21:193-202
McManus, C Joel; Coolon, Joseph D; Duff, Michael O et al. (2010) Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res 20:816-25
McManus, C Joel; Duff, Michael O; Eipper-Mains, Jodi et al. (2010) Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci U S A 107:12975-9
Nilsen, Timothy W; Graveley, Brenton R (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature 463:457-63
Hale, Caryn R; Zhao, Peng; Olson, Sara et al. (2009) RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139:945-56

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