Details

COMPILATION OF mRNA POLYADENYLATION SIGNALS IN ARABIDOPSIS THALIANA REVEALED NEW SIGNAL ELEMENTS AND POTENTIAL SECONDARY STRUCTURES

by Loke, Johnny Chee

Abstract (Summary)
Plant messenger RNA (mRNA) polyadenylation is a critical step in gene expression. The cis-elements directing the cleavage and polyadenylation process are poorly understood. Using a novel algorithm SignalSleuth and a database containing authenticated polyadenylation sites, I have analyzed the composition of mRNA polyadenylation signals of 17,000 genes from a model plant Arabidopsis thaliana. Besides compiling extensive lists of different size patterns of Far-Upstream-Element (FUE) and Near-Upstream-Element (NUE) signals, two new sets of polyadenylation signals were discovered: one flanking the cleavage site, termed Cleavage-Element (CE); the other located downstream of the cleavage site termed Far-Downstream-Element (FDE). The nucleotide composition-profile scan of 3’-untranslated-region and the downstream sequences unveiled a distinct arrangement of alternate stretches of U and A nucleotides, leading to a hypothesis of secondary structure formation. Indeed, secondary structures were predicted by mFold algorithm, and maintenance of these structures was found to be important in polyadenylation using data compiled from literature.
Bibliographical Information:

Advisor:

School:Miami University

School Location:USA - Ohio

Source Type:Master's Thesis

Keywords:keywords polyadenylation signal mrna 3 end formation secondary structures bioinformatics termination downstream element

ISBN:

Date of Publication:01/01/2004

© 2009 OpenThesis.org. All Rights Reserved.