Računalna analiza dugih nekodirajućih RNA ogulinske špiljske spužvice (Eunapius subterraneus)

master's thesis

• Title (english): Computational analysis of long non-coding RNA in endemic cave sponge (Eunapius subterraneus)
• Author: Kristian Bodulić
• 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: 2020-09-18, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Pojavom metoda sekvenciranja druge generacije, duge nekodirajuće RNA postale su vrlo zanimljiv predmet bioloških istraživanja. Njihove uloge dokazane su u velikom broju bioloških procesa, od kojih je najvažnije spomenuti regulaciju ekspresije brojnih gena. Ipak, ova skupina RNA još uvijek nije istražena u brojnim koljenima životinja, uključujući i spužve. Radi bolje karakterizacije navedene skupine RNA spužvi, u ovom istraživanju korištene su dvije sekvencirane knjižnice RNA primarnih kultura ogulinske špiljske spužvice. Serijom bioinformatičkih metoda u sastavljenim transkriptomima pronađen je velik broj dugih nekodirajućih RNA. Utvrđeno je postojanje brojnih sličnih svojstava dugih nekodirajućih RNA spužvi i drugih životinjskih koljena, uključujući izrezivanje introna, mogućnost alternativnog prekrajanja i pristranost u sastavu nukleotida. Također, ustanovljena je potencijalna uloga transpozona u nastanku dugih nekodirajućih RNA, kao i moguća uloga navedene skupine RNA u regulaciji ekspresije brojnih protein-kodirajućih gena. Isto tako, opisan je raznolik skup stabilnih sekundarnih struktura dugih nekodirajućih RNA. Na kraju, pronađena je relativno slaba očuvanost dugih nekodirajućih RNA u koljenu spužvi, pri čemu iznimku čini izrazito velika sličnost navedene skupine RNA ogulinske špiljske spužvice i srodne spužve Ephydatia mulleri, što baca novo svjetlo na raspravu o mogućnosti pogrešne klasifikacije ogulinske špiljske spužvice.

Abstract (english)

With the advances in next-generation sequencing technologies, long non-coding RNA have become one of the focal points of RNA research. Their roles have been demonstrated in a plethora of biological processes, most important being the regulation of gene expression. However, key information surrounding this type of RNA in many phyla is missing, which is why this research focused on characterizing long non-coding RNAs in sponges (Porifera). In this study, I used two RNA libraries isolated from the endemic cave sponge to identify a comprehensive set of highly-confident long non-coding RNAs. This study showed many similarities between long non-coding RNAs of sponges and other animals, including the phenomena of intron excision, alternative splicing, and nucleotide content bias. Furthermore, this research demonstrated the potential role of transposable elements in the origin of sponges' long non-coding RNAs, as well as a possible role of these RNAs in the regulation of expression of many important genes. Finally, this study found a low level of conservation of sponges' long non-coding RNAs, with the exception of the similarity found between endemic cave sponge and a closely related sponge, Ephydatia mulleri, which sheds new light on the potential misclassification of the endemic cave sponge.

• Keywords: nekodirajući dijelovi genoma; koljeno spužvi; transkriptom; transpozoni; očuvanost RNA
• Keywords (english): non-coding genomic elements; phylum Porifera; transcriptome; transposones; RNA conservation
• Language: croatian
• URN:NBN: urn:nbn:hr:217:310016
• 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: 2020-09-24 08:27:55