Date of Award

Summer 8-2010

Document Type


Degree Name

Master of Science (MS)


Biological Sciences

First Advisor

Munroe, Stephen

Second Advisor

McNally, Mark

Third Advisor

Anderson, James


In eukaryotes, alternative splicing is an essential post transcriptional modification process for functional gene expression and a major contributor to protein diversity. The regulation of alternative splicing generally involves the engagements of RNA sequences cis-acting elements) and corresponding protein factors (trans-acting factors). The cisacting RNA motifs can be categorized depending on positional and functional differences. Trans-acting protein factors will then bind to RNA sequences and affect the corresponding splicing activity. Recently, factors associated with 3’ polyadenylation have also been identified to affect alternative splicing.

In mammals, the α-thyroid hormone receptor gene (TRα) produces transcripts for two functionally antagonistic isoforms, TRα1 and TRα2 by alternative splicing of pre-mRNA. TRα1 will activate the thyroid hormone responsive genes after the binding of thyroid hormone while TRα2, a non-hormone binding variant, plays a functionally antagonistic role. A third minor isoform, TRα3 has also been described which is similar to TRα2 but lacks part of the terminal sequence. Regulation of TRα alternative splicing requires the interaction of cis-trans elements and alternative polyadenylation. The goal of my project is to study the regulatory mechanism of TRα alternative splicing.

In our system, ESX10 (exonic splicing enhancer on exon10) was previously identified as a 200 nt splicing enhancer element located on the last exon of TRα gene. My study further characterized the enhancing capability of exonic splicing enhancers (ESE) motifs within ESX10. Three heptanucleotide ESE motifs in the 3’ half of ESX10 have been identified. In vitro experiments indicate that substitution of eight nucleotides within three heptamers decreases the enhancing capability of ESX10. After substitution of ESX10 and its subfragments with Rev-erbβ sequence, cryptic splicing was detected and quantitated. Previous experiments also indicate that replacing original TRα1 and TRα2 poly (A) site with a strong SVL poly (A) signal would increase the corresponding mRNA expression. My results show that introduction of downstream poly (A) signal increases splicing fidelity. When upstream 5’ss of TRα2 is disabled, the strong poly (A) signal enhances the usage of weak splicing cites and promote cryptic splicing.