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master's thesis
Računalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ
Zagreb: University of Zagreb, Faculty of Science, 2020. urn:nbn:hr:217:579531
Štancl, Paula
University of Zagreb
Faculty of Science
Department of Biology

Institutional repository: Repository of the Faculty of Science

Cite this document

Štancl, P. (2020). Računalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ (Master's thesis). Zagreb: University of Zagreb, Faculty of Science. Retrieved from https://urn.nsk.hr/urn:nbn:hr:217:579531

Štancl, Paula. "Računalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ." Master's thesis, University of Zagreb, Faculty of Science, 2020. https://urn.nsk.hr/urn:nbn:hr:217:579531

Štancl, Paula. "Računalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ." Master's thesis, University of Zagreb, Faculty of Science, 2020. https://urn.nsk.hr/urn:nbn:hr:217:579531

Štancl, P. (2020). 'Računalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ', Master's thesis, University of Zagreb, Faculty of Science, accessed 22 November 2024, https://urn.nsk.hr/urn:nbn:hr:217:579531

Štancl P. Računalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ [Master's thesis]. Zagreb: University of Zagreb, Faculty of Science; 2020 [cited 2024 November 22] Available at: https://urn.nsk.hr/urn:nbn:hr:217:579531

P. Štancl, "Računalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ", Master's thesis, University of Zagreb, Faculty of Science, Zagreb, 2020. Available at: https://urn.nsk.hr/urn:nbn:hr:217:579531

Metadata
TitleRačunalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ
Title (english)Computational analysis of MT retrotransposons in mouse strains C57BL/6J and PWK/Phj
AuthorPaula Štancl
MentorKristian Vlahoviček (mentor)
Committee memberKristian Vlahoviček (predsjednik povjerenstva)
Committee memberDamjan Franjević (član povjerenstva)
Committee memberDuje Lisičić (član povjerenstva)
Committee memberRosa Karlić (član povjerenstva)
GranterUniversity of Zagreb
Faculty of Science
(Department of Biology)
Zagreb
Defense date and country2020-07-16, Croatia
Scientific / art field,
discipline and subdiscipline		NATURAL SCIENCES
Biology
Abstract
Retrotranspozoni MT pripadaju klasi LTR retrotranspozona, specifičnih za glodavce. Cjeloviti MT elementi sadrže dva duga terminalna ponavljanja (engl. long terminal repeat, LTR) i internu sekvencu. Zbog ektopične rekombinacije, izrezuje se interna sekvenca cjelovitog MT elementa stvarajući samostalni LTR. Standardna anotacija retrotranspozona radi se programom RepeatMasker, čiji je glavni nedostatak precizna anotacija cjelovitih elemenata. Cilj ovog diplomskog rada bio je poboljšati već postojeću anotaciju cjelovitih MT elemenata dobivenih upotrebom programa RepeatMasker i identificirati homologne MT elemente između klasičnog C57BL/6J i divljeg PWK/PhJ mišjeg soja. Razvijena računalna metoda anotacije cjelovitih MT elemenata usredotočena je na filtriranje njihovih očuvanih duljina LTR-ova i rezultirala je većim brojem anotiranih cjelovitih MT elemenata u C57BL/6J genomu za razliku od PWK/PhJ genoma. Filogenetski mlađi i jedini aktivni cjeloviti MT elementi, MTA i MTB, imali su više novih specifičnih elemenata kod C57BL/6J soja, koji su se pojavili nakon razdvajanja sojeva, dok su stariji MT elementi očuvani među mišjim sojevima. Integracije očuvanih i specifičnih MT elemenata kod sojeva većinom su u intronima protein-kodirajućih gena. Identificirani novi specifični elementi C57BL/6J soja integrirani su u egzone gena olfaktornih receptora te mogu pridonijeti fenotipskim razlikama između mišjih sojeva C57BL/6J i PWK/PhJ.
Abstract (english)
Rodent-specific MT retrotransposons belong to a class of LTR retrotransposons. Full-length MT elements contain two long terminal repeats (LTRs) and an internal sequence. Due to ectopic recombination, the internal sequence of full-length MT elements is excised producing a solo LTR. The standard annotation of retrotransposons is done with RepeatMasker program which one of the major drawbacks is the precise annotation of full-length elements. The goal of this thesis was to improve the RepeatMasker annotation of MT elements and to identify homologous between a classical mouse strain C57BL/6J and a wild-derived mouse strain PWK/PhJ. The developed computational method focuses on the conserved length of their LTRs and has resulted in a larger number of annotated full-length MT elements in in the mouse strain C57BL/6J. Phylogenetically younger and still active annotated full-length MT elements, MTA and MTB, had more new C57BL/6J-strains specific elements that have emerged after the separations of the strains. On the other hand, older MT elements were more conserved among strains. Conserved and strain-specific MT element integrations into genes mostly occurred in introns of protein-coding genes. Identified new C57BL/6J-strains specific elements integrated into exons of olfactory receptor genes, may contribute to phenotypic differences between mouse strains C57BL/6J and PWK/PhJ.
Keywords
Keywords (english)
Languagecroatian
URN:NBNurn:nbn:hr:217:579531
Study programmeTitle: Molecular Biology
Study programme type: university
Study level: graduate
Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
Type of resourceText
File originBorn digital
Access conditionsOpen access
Terms of useLicence In copyright icon
Created on2020-07-23 12:06:32