Računalna analiza retrotranspozona MT kod sojeva miševa C57BL/6J i PWK/PHJ

master's thesis

• Title (english): Computational analysis of MT retrotransposons in mouse strains C57BL/6J and PWK/Phj
• Author: Paula Štancl
• Mentor: Kristian Vlahoviček (mentor)
• Committee member: Kristian Vlahoviček (predsjednik povjerenstva)
• Committee member: Damjan Franjević (član povjerenstva)
• Committee member: Duje Lisičić (član povjerenstva)
• Committee member: Rosa Karlić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2020-07-16, 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: LTR retrotranspozoni; sojevi miševa; računalna genomika
• Keywords (english): LTR retrotransposons; mouse strains; computational genomics
• Language: croatian
• URN:NBN: urn:nbn:hr:217:579531
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2020-07-23 12:06:32