Pre-mRNA splicing is a fundamental process required for the expression of most metazoan genes. Defects in splicing lead to many human genetic diseases, and pre-mRNAs containing multiple introns and exons can be alternatively spliced in a cell type, cell cycle, or developmentally regulated manner by joining different pairs of 5'and 3'splice sites. Insights into the basic mechanisms of pre-mRNA splicing and splice site recognition are therefore fundamental to understanding regulated gene expression and human disease. The overall goal of this research proposal is to understand the mechanisms involved in splice-site recognition and pairing of pre-mRNAs. During the previous funding period, we have developed quantitative assays to provide new insights into the mechanisms of splice-site pairing. In the next phase of investigation, we propose to determine the ?molecular events that lock splice sites into a pairing position and to analyze how the combinatorial contribution of multiple splicing signals influence exon inclusion. Specifically, we will determine the biochemical steps that lead to splice-site pairing in A complex (Aim 1). We will test the hypothesis that ATP hydrolysis during A complex formation drives the irreversible juxtaposition of alternative splice sites or exons.
In Aim 2 we will determine how the spliceosome executes commitment to splice-site pairing. We will use immuno-depletion and RNAi approaches to test the hypothesis that a subset of U2 snRNP components and associated proteins (CUS2/Tat-SF-1, Prp5, SF3a120, and UAP56) is necessary for irreversible splice-site pairing.
Aim 3 describes a systematic and quantitative approach to determine how the probability of exon definition and inclusion is influenced by the combinatorial contributions of variable splice sites, enhancers, silencers, and the exon/intron architecture. We will test the hypothesis that measures of exon inclusion can be quantitated and used to improve the predictability of constitutive and alternative splicing within the human genome. These experiments are important because 1) the commitment to splice-site pairing constitutes arguably the most crucial step during the splicing reaction because it determines the splicing patterns of pre- mRNAs, and because 2) a quantitative framework of combinatorial exon recognition will elucidate mechanisms of splicing regulation and allow to predict the intrinsic pattern of splicing from sequence analysis.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Bender, Michael T
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Irvine
Schools of Medicine
United States
Zip Code
Garibaldi, Angela; Carranza, Francisco; Hertel, Klemens J (2017) Isolation of Newly Transcribed RNA Using the Metabolic Label 4-Thiouridine. Methods Mol Biol 1648:169-176
Movassat, Maliheh; Shenasa, Hossein; Hertel, Klemens J (2017) Preparation of Splicing Competent Nuclear Extract from Mammalian Cells and In Vitro Pre-mRNA Splicing Assay. Methods Mol Biol 1648:11-26
Aubol, Brandon E; Wu, Guowei; Keshwani, Malik M et al. (2016) Release of SR Proteins from CLK1 by SRPK1: A Symbiotic Kinase System for Phosphorylation Control of Pre-mRNA Splicing. Mol Cell 63:218-228
Movassat, Maliheh; Crabb, Tara L; Busch, Anke et al. (2016) Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns. RNA Biol 13:646-55
Mueller, William F; Larsen, Liza S Z; Garibaldi, Angela et al. (2015) The Silent Sway of Splicing by Synonymous Substitutions. J Biol Chem 290:27700-11
Busch, Anke; Hertel, Klemens J (2015) Splicing predictions reliably classify different types of alternative splicing. RNA 21:813-23
Webb, Chiu-Ho T; Hertel, Klemens J (2014) Preparation of splicing competent nuclear extracts. Methods Mol Biol 1126:117-21
Mueller, William F; Hertel, Klemens J (2014) Kinetic analysis of in vitro pre-mRNA splicing in HeLa nuclear extract. Methods Mol Biol 1126:161-8
Morris 4th, John P; Greer, Renee; Russ, Holger A et al. (2014) Dicer regulates differentiation and viability during mouse pancreatic cancer initiation. PLoS One 9:e95486
Movassat, Maliheh; Mueller, William F; Hertel, Klemens J (2014) In vitro assay of pre-mRNA splicing in mammalian nuclear extract. Methods Mol Biol 1126:151-60

Showing the most recent 10 out of 41 publications