Dissertation/Thesis Abstract

Genome-wide analysis of splicing requirements and function through mRNA profiling
by Heimiller, Joseph Karl, Ph.D., University of Colorado at Boulder, 2013, 112; 3607314
Abstract (Summary)

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.

Indexing (document details)
Advisor: Singh, Ravinder
Commitee: Dowell, Robin D., Goldberg, Debra S., Leinwand, Leslie A., Yi, Rui
School: University of Colorado at Boulder
Department: Molecular, Cellular and Developmental Biology
School Location: United States -- Colorado
Source: DAI-B 75/04(E), Dissertation Abstracts International
Subjects: Biology, Molecular biology, Bioinformatics
Keywords: Nucleotide composition, PTB, RNA splicing, Splicing modeling, U2AF
Publication Number: 3607314
ISBN: 9781303648441
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