Alternative pre-mRNA splicing is a common mechanism for regulating gene expression in metazoans. Indeed, RNA processing is a conduit by which genomic information is transferred to proteomic information. In fact, it is now recognized that 40-50% of the known human and mouse disease gene mutations affect the splicing process. Thus, understanding how introns are recognized and how patterns of alternative splicing are set up may allow therapeutic intervention. The overall objective of the research proposed in this grant is to elucidate biochemical mechanisms used to regulate splicing of messenger RNA precursors (pre-mRNA) during development in the fruit fly,Drosophila melanogaster. Our efforts will be focused on understanding two examples of alternative splicing in detail and, more generally, the role that RNA binding proteins play in controlling splicing patterns. In order to accomplish our overall objectives, we will: 1. Purify and analyze nuclear pre-mRNPs that contain the Drosophila hnRNP proteins, PSI, hrp48, hrp40, hrp38 and hrp36. 2. Investigate the splicing regulation of the P element and squid/hrp40 pre-mRNAs using biochemical studies. 3. Analyze the genome-wide effects on alternative pre-mRNA splicing patterns after removal of specific RNA binding splicing factors using Drosophila splice junction microarrays. 4. Analyze the structure and function of PSI, Drosophila U2AF and U2AF-related proteins.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM061987-17
Application #
7327810
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Greenberg, Judith H
Project Start
1991-07-01
Project End
2009-12-31
Budget Start
2008-01-01
Budget End
2008-12-31
Support Year
17
Fiscal Year
2008
Total Cost
$340,136
Indirect Cost
Name
University of California Berkeley
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Francis, Malik Joseph; Roche, Siobhan; Cho, Michael Jeffrey et al. (2016) Drosophila IRBP bZIP heterodimer binds P-element DNA and affects hybrid dysgenesis. Proc Natl Acad Sci U S A 113:13003-13008
Majumdar, Sharmistha; Rio, Donald C (2015) P Transposable Elements in Drosophila and other Eukaryotic Organisms. Microbiol Spectr 3:MDNA3-0004-2014
Horan, Lucas; Yasuhara, Jiro C; Kohlstaedt, Lori A et al. (2015) Biochemical identification of new proteins involved in splicing repression at the Drosophila P-element exonic splicing silencer. Genes Dev 29:2298-311
Taliaferro, J Matthew; Marwha, Dhruv; Aspden, Julie L et al. (2013) The Drosophila splicing factor PSI is phosphorylated by casein kinase II and tousled-like kinase. PLoS One 8:e56401
Majumdar, Sharmistha; Singh, Anita; Rio, Donald C (2013) The human THAP9 gene encodes an active P-element DNA transposase. Science 339:446-8
Taliaferro, J Matthew; Aspden, Julie L; Bradley, Todd et al. (2013) Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression. Genes Dev 27:378-89
Pastuszak, Alexander W; Joachimiak, Marcin P; Blanchette, Marco et al. (2011) An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res 39:2344-56
Taliaferro, J Matthew; Alvarez, Nehemiah; Green, Richard E et al. (2011) Evolution of a tissue-specific splicing network. Genes Dev 25:608-20
Brooks, Angela N; Aspden, Julie L; Podgornaia, Anna I et al. (2011) Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. RNA 17:1884-94
Hellsten, Uffe; Aspden, Julie L; Rio, Donald C et al. (2011) A segmental genomic duplication generates a functional intron. Nat Commun 2:454

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