The correct secondary structures and the relationships of structural elements to the function of snRNAs in splicing have been appreciated for a number of years. Roles of snRNAs in recognition of each other and the premessenger RNA reactive sites that establish the structure of the active spliceosome have been demonstrated. A continuing mystery in the analysis of splicing is how the snRNA rearrangements are achieved and coordinated during assembly of the spliceosome, catalysis, and disassembly. A second major issue concerns how, at the biochemical level, the regulation of splicing impinges on the basic process of spliceosome assembly. A third and emerging set of questions concerns the role of splicing in genome function and evolution. Experiments addressing each of these major questions are proposed. By characterizing the functional interactions between U2 snRNA, the DExD/H ATPase Prp5p and Cus2p, the enforcer of ATP-dependence at the Prp5p step it will be possible to understand the mechanism of prespliceosome assembly. Critical to this process, the yeast SF3a (Prp9p, Prp11p, Prp21p), and SF3b (Cus1p, Hsh49p, Hsh155p, Rse1p) protein complexes are present near the catalytic core of the spliceosome. The hypothesis is that protein factors that interact with U2 snRNA play essential roles in the regulation, progression and fidelity of splicing reactions. A unique opportunity to study positive regulation of splicing is by exploring the functional interactions between Mer1p and the U1 snRNP during splicing activation. The hypothesis is that Mer1p accelerates a key step in spliceosome assembly or splicing. Finally a modified microarray technology capable of monitoring all introns in the yeast genome in parallel will be applied to questions concerning the global regulation of splicing. The results should reveal general features of presliceosome assembly in terms of the basal machinery at the key step of prespliceosome formation, and in instances of splicing regulation. Genome-wide views of splicing have never been developed, and the new technology will allow this important process to be understood in terms of regulatory networks. These studies will be important foundations for investigations into systems with more complex splicing, such as human cells.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM040478-15
Application #
6622037
Study Section
Cell Development and Function Integrated Review Group (CDF)
Program Officer
Rhoades, Marcus M
Project Start
1988-07-01
Project End
2005-11-30
Budget Start
2002-12-01
Budget End
2003-11-30
Support Year
15
Fiscal Year
2003
Total Cost
$474,971
Indirect Cost
Name
University of California Santa Cruz
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
125084723
City
Santa Cruz
State
CA
Country
United States
Zip Code
95064
Lucas, Bronwyn A; Lavi, Eitan; Shiue, Lily et al. (2018) Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay. Proc Natl Acad Sci U S A 115:968-973
Fagg, W Samuel; Liu, Naiyou; Fair, Jeffrey Haskell et al. (2017) Autogenous cross-regulation of Quaking mRNA processing and translation balances Quaking functions in splicing and translation. Genes Dev 31:1894-1909
de Bruin, Ruben G; Shiue, Lily; Prins, Jurriƫn et al. (2016) Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression. Nat Commun 7:10846
Johnson, Tracy L; Ares Jr, Manuel (2016) SMITten by the Speed of Splicing. Cell 165:265-7
Simmons, Melinda P; Bachy, Charles; Sudek, Sebastian et al. (2015) Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations. Mol Biol Evol 32:2219-35
Ares Jr, Manuel (2015) Coffee with Ribohipster. RNA 21:494-6
Fu, Xiang-Dong; Ares Jr, Manuel (2014) Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 15:689-701
Paz, Inbal; Kosti, Idit; Ares Jr, Manuel et al. (2014) RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res 42:W361-7
Turner, Rushia; Shefer, Kinneret; Ares Jr, Manuel (2013) Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7). RNA 19:1857-63
Effenberger, Kerstin A; Perriman, Rhonda J; Bray, Walter M et al. (2013) A high-throughput splicing assay identifies new classes of inhibitors of human and yeast spliceosomes. J Biomol Screen 18:1110-20

Showing the most recent 10 out of 50 publications