Date of Award
Spring 1-1-2013
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
First Advisor
Leslie A. Leinwand
Second Advisor
Ravinder Singh
Third Advisor
Robin D. Dowell
Fourth Advisor
Debra S. Goldberg
Fifth Advisor
Rui Yi
Abstract
The RNA-binding proteins U2AF and PTB play important roles in gene expression in many eukaryotic species. Although U2AF and PTB have been well-studied, their functional requirements have not been investigated on a genome-wide scale. In this thesis, I analyze RNA expression data to determine the requirement of the general splicing factor U2AF in S. pombe and to identify genes misregulated in Drosophila PTB mutants. I find that many introns are insensitive to U2AF inactivation in a Schizosaccharomyces pombe U2AF59 mutant, prp2.1. Bioinformatics analysis indicates that U2AF-insensitive introns have stronger 5' splice sites and higher A/U composition. The importance of intronic nucleotide composition was further investigated using wild type RNA expression data sets. I show that nucleotide composition is a relatively important factor for regulated intron retention in a variety of species. I also analyzed the RNA-binding protein PTB using RNA Seq data to reveal genes misregulated in PTB mutants in D. melanogaster. I identify misregulation of alternative splicing in PTB mutants and putative PTB binding sites. In the PTB embryonic lethal mutant, which shows dorsoventral patterning defects, I show that dorsal fate genes are significantly up-regulated. I present a model to link PTB to dorsal closure defects. This thesis provides the first genome-wide analysis of U2AF in S. pombe and PTB in Drosophila melanogaster.
Recommended Citation
Heimiller, Joseph Karl, "Genome-Wide Analysis of Splicing Requirements and Function through mRNA Profiling" (2013). Molecular, Cellular, and Developmental Biology Graduate Theses & Dissertations. 57.
https://scholar.colorado.edu/mcdb_gradetds/57
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