Computational analysis of mRNA polyadenylation patterns in vertebrate genomes

Barilar, Ivan (2012) Computational analysis of mRNA polyadenylation patterns in vertebrate genomes. Diploma thesis, Faculty of Science > Department of Biology.

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Abstract

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease of motor neurons. Affected motor neurons accumulate misshapen and insoluble proteins in proteinaceous inclusions within axons and cell bodies. One of the proteins present in those inclusions is TDP-43. That protein among other things has a role in gene expression. During the polyadenylation process it binds to the GU-rich element of the 3’ UTR region of b-adducin mRNA. In the absence of the protein there is a significant drop observed in the expression levels of b-adducin. The goal of this research was to find out if other genes have similar polyadenylation motifs as badducin, that could bind TDP-43, by using bioinformatics tools. The data used in the project (8 vertebrate genomes) was obtained from the Ensembl genome database. I wrote 17 scripts using the Perl programming language and Ensembl Perl API to isolate around 600 genes from the human genome that could possibly be regulated by TDP-43. Nine of those genes have been described in previous work done on the ALS to have different expression levels in patients with ALS. Additionally, evolutionary conservation of the polyadenylation signal and GU-rich element was observed in other vertebrate species.

Item Type: Thesis (Diploma thesis)
Keywords: ALS, TDP-43, poly(A) motif, bioinformatics, Ensembl
Supervisor: Vlahoviček, Kristian
Date: 2012
Number of Pages: 40
Subjects: NATURAL SCIENCES > Biology
Divisions: Faculty of Science > Department of Biology
Depositing User: Grozdana Sirotic
Date Deposited: 27 May 2014 11:42
Last Modified: 27 May 2014 11:42
URI: http://digre.pmf.unizg.hr/id/eprint/1787

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