A bioinformatics tool to detect physical gene clusters in functional genomics data

Conradie, Louis Timoteus (2021-03)

Thesis (MSc)--Stellenbosch University, 2021.

Thesis

ENGLISH ABSTRACT: Many studies have investigated the biological effects of the external environment on the genetic expression of a living cell. This particular study looks at gene clusters that are switched on at a series of discrete time points when Saccharomyces cerevisiae comes out of stationary phase, when the cell is fed a carbon source after a starvation period. To achieve this, Pyxis2 was developed, a bioinformatics tool that is able to detect gene clusters in functional genomics data from any organism. The program detects physical clusters of genes that share a defined functional genomic property, such as transcriptional activity, that may be interpreted in terms of a biological functionality. Pyxis2 provides several options to the user that may be adjusted for appropriate levels of sensitivity. Pyxis2 is available at https://github.com/Louis-Conradie/Pyxis2_classes_2020. Following the identification of gene clusters that are induced during the exit of stationary phase in yeast, the study is extended to also investigate the biological relationship between the identified genes and possible regulatory mechanisms. These mechanisms may include transcriptional activators and co-activators, epigenetic modifications such as histone H3K9ac acetylation, or the effect of the domain wide change of the spatial structure of chromatin. I show that the mega-Dalton transcriptional activation complex SAGA is associated with some of the transcriptionally induced clusters at early times during stationary phase exit, and that acetylation of lysine 9 of histone H3 is not a detectable property of active clusters. I finally show some association between spatial proximity of parts of the genome and cluster gene induction but find this association in cycling cells as opposed to in cells re-engaging passage through the cell-cycle. I finally discuss the implications of my findings in the context of the current literature and identify future avenues of enquiry.

AFRIKAANSE OPSOMMING: Verskeie studies het die biologiese effek van die eksterne omgewing op die genetiese uitdrukking in ‘n lewendige sel ondersoek. Hierdie spesifieke studie kyk na geen klusters wat na diskrete tyd periodes aangeskakel word wanneer Saccharomyces cerevisiae uit stasionêre fase uitkom nadat die sel na ‘n verhongering periode met ‘n koolstof bron gevoer is. Om dit te bereik is Pyxis2 ontwikkel, ‘n bioinformatika toepassing wat die vermoë het om geen klusters in funksionele genomiese data van enige organisme te identifiseer. Die program identifiseer fisiese klusters van gene wat ‘n funksionele genomika eienskap deel. Soos transkripsionêle aktiwiteit, wat binne ‘n breër biologiese funksionaliteit geïnterpreteer mag word. Pyxis2 verskaf verskeie opsies aan die gebruiker wat verstel mag word vir geskikte vlakke van sensitiwiteit. Pyxis2 is beskikbaar by https://github.com/Louis-Conradie/Pyxis2_classes_2020. Na die identifisering van geen klusters wat die geïnduseer is gedurende die verlating van stasionêre fase in gis, is die studie uitgebrei om ook die biologiese verwantskap tussen die geïdentifiseerde gene en moontlike regulatoriese meganismes te ondersoek. Hierdie meganismes kan transkripsionêle aktiveerders en ko-aktiveerders insluit, epigenetiese modifikasies soos H3K9ac, of die effek van die domein wye verandering in die ruimtelike struktuur van chromatien. Ek wys dat die mega-Dalton transkripsionêle aktiveerder SAGA kompleks met sommige van die aktiewe klusters tydens vroeë tye met die verlaat van stasionêre fase geassosieerd is, en dat die asetilering van lisien 9 van histoon H3 nie ‘n waarneembare eienskap van aktiewe klusters is nie. Ek toon finaal ‘n assosiasie tussen die ruimtelike nabyheid van gedeeltes van die genoom en kluster geen induksie, maar vind hierdie assosiasie in selle wat deur die sel siklus roteer eerder is in selle wat die sel siklus betree. Ek bespreek finaal die implikasies van my bevindinge in die konteks van die huidige literatuur, en identifiseer moontlike toekomstige paaie van ondersoek.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/109883
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