Zastupljenost palindroma u kodirajućoj DNA kvasca Saccharomyces cerevisae

master's thesis

• Title (english): Distribution of palindromic sequences in coding DNA of yeast Saccharomyces cerevisiae
• Author: Ranko Gaćeša
• Mentor: Ivan-Krešimir Svetec (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Laboratory for Biology and Microbial Genetics); Zagreb
• Defense date and country: 2011-11-04, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Dosadašnja istraživanja ukazuju na zaključak da su palindromske sekvencije u molekuli DNA nužne za funkcioniranje genoma jer se često nalaze u bis-djelujućim regijama, ali istovremeno predstavljaju ozbiljnu opasnost za genetičku stabilnost, pri čemu genetička nestabilnost palindroma raste s njihovom duljinom. Ovakva dvojaka biološka uloga palindroma u molekuli DNA potaknula je bioinformatička istraživanja sekvencioniranih genoma s ciljem da se ustanovi broj, duljina i raspored svih palindroma. Međutim, do sada još nije nedvojbeno ustanovljeno da li broj palindroma u nekom genomu odstupa od očekivane vrijednosti, te što bi mogao biti uzrok tom odstupanju. U ovakvim istraživanjima osnovnu prepreku predstavlja upravo određivanje očekivanoga broja palindroma jer na redoslijed nukleotida pa tako i na mogućnost pojave palindroma utječu AT/GC-sastav i „pristrana uporabu kodona“ (eng. codone usage bias) kao i činjenica da genom mora kodirati za odgovarajući proteom. U ovom radu razvijen je računalni program za određivanje očekivanog broja palindroma u kodirajućoj DNA. Ovaj program osniva se na uspoređivanju broja palindroma u zadanoj sekvenciji i u računalno generiranim sekvencijama koje se od zadane sekvencije razlikuju samo po položaju sinonimnih kodona. Rezultati ovog rada jasno ukazuju na zaključak da kodirajuća DNA kvasca S. cerevisiae sadrži manje palindroma nego što bi se to statistički očekivalo te da je zastupljenost palindroma u kodirajućoj DNA u negativnoj korelaciji s razinom ekspresije gena.

Abstract (english)

Palindrome sequences in DNA are necessary for proper genome function due to their role in cis-regulating regions. However these sequences pose threat to integrity of genome due to their affinity toward formation of secondary structures. Prompted by dual nature of palindromes in DNA, bioinformatical studies were performed to determine their position, length and distribution in genomes of various organisms. Nonetheless, none of these studies managed to provide method for quick and accessible calculation of expected number of palindromes in every single ORF of studied genome. Difficulty of these studies is attributed to fact that AT/GC content of sequence, codon usage bias and polypeptide product of DNA sequence all play role in distribution of nucleotides in the sequence and therefore its palindrome content. We have developed computer program for automatic calculation of expected number of palindromes in coding DNA sequence and used it to compute difference between real and expected number of palindromes in entire coding DNA of yeast Saccharomyces cerevisiae. Functionality of this program is based on random exchange of synonymous codons in studied sequence and therefore preserves codon usage bias and polypeptide product of studied sequence. Results of this study demonstrate that coding DNA of yeast contains significantly lower number of palindromes then would be expected and that number of palindromes in genes negatively correlates with gene expression.

• Keywords: kvasac Saccharomyces cerevisiae; palindrom; DNA; genom; sinonimni kodoni; ekspresija gena
• Keywords (english): synonymous codons; palindrome; yeast Saccharomyces cerevisiae; gene expression; genome
• Language: croatian
• URN:NBN: urn:nbn:hr:159:138146
• Study programme: Title: Biotechnology; specializations in: Biochemical-Microbiology; Course: Biochemical-Microbiology; Study programme type: university; Study level: graduate; Academic / professional title: diplomirani inženjer biotehnologije; smjer biokemijsko-mikrobiološki (diplomirani inženjer biotehnologije; smjer biokemijsko-mikrobiološki)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Access restricted to students and staff of home institution
• Created on: 2017-05-31 07:52:36