Analiza ekspresije genske regulacije tijekom ranog razvoja miša

master's thesis

• Title (english): Time series analysis of gene expression regulation profiles in early mouse development
• Author: Zrinko Kozić
• Mentor: Kristian Vlahoviček (mentor)
• Committee member: Kristian Vlahoviček (predsjednik povjerenstva)
• Committee member: Gordana Lacković-Venturin (član povjerenstva)
• Committee member: Branimir Bertoša (član povjerenstva)
• Committee member: Mirjana Kalafatić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2013-09-19, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

Rani, predimplantacijski, period razvoja sisavaca obuhvaća razdoblje od oplodnje jajne stanice do implantacije blastociste u stijenku maternice. U tom su periodu aktivni razni oblici genske regulacije i ona se, osim na transkripcijskoj, odvija na više razina. Regulacija genske ekspresije kroz razvojne stadije je vrlo dinamična i poznato je nekoliko događaja genskih aktivacija i inaktivacija. Istraživanja regulacije genske ekspresije tijekom razvoja provode se pomoću analize ekspresije u vremenskom slijedu. Metoda sekvenciranja stanične mRNA (RNA-seq) omogućuje nepristranu analizu transkriptoma i kvantifikaciju ekspresije. Analizirao sam rezultate RNA-seq eksperimenata koristeći stanice miša u uzastopnim stadijima razvoja od primarne oocite do blastule. Nakon kvantifikacije ekspresije, identificirao sam diferencijalno eksprimirane gene koje sam metodama nenadgledanog strojnog učenja grupirao u ekspresijske profile. Nad profilima sam proveo funkcionalnu anotaciju i analizu obogaćenja motiva prepoznatih od transkripcijskih faktora. Rezultati pokazuju da se na ovaj način mogu grupirati geni s promjenama u ekspresiji u određenim stadijima te su profilima pridodani funkcionalni elementi koji mogu biti povezani uz regulaciju ekspresije. Također sam identificirao transkripcijske faktore koji utječu na ekspresiju pojedinih profila.

Abstract (english)

Mammalian preimplantation development is a period starting with the fertilization of the oocyte and ending with the implantation of blastocyst into the wall of the uterus. This is a period where dynamic changes in gene expression are regulated through various mechanisms, which act on both transcriptional and non-transcriptional levels. High-throughput research of genetic regulation during development is done in form of time-course expression analysis. RNA-seq is a method of sequencing the total cellular mRNA and provides a capability of unbiased transcriptome analysis and expression quantification. Mouse cells in early developmental stages were analysed using RNA-seq in order to quantify the expression through the time-course. I identified differentially expressed genes and clustered them into expression profiles using unsupervised machine learning methods. I searched the profiles for enrichment of functional elements and sequence motifs recognized by DNA binding transcription factors. Results show that genes can be clustered by their expression patterns into distinct groups, thus enabling the observation of significant changes in expression. Functional elements related to gene expression were assigned to profiles. Finally, I identified the transcription factors that may influence the regulation of expression.

• Keywords: RNA-seq; ekspresijsko profiliranje; k-means; funkcionalna anotacija; obogaćenje motiva; transkripcijski faktori
• Keywords (english): RNA-seq; expression profiling; k-means; functional annotation; motif enrichment; transcription factors
• Language: croatian
• URN:NBN: urn:nbn:hr:217:604911
• 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: Access restricted to students and staff of home institution
• Created on: 2017-04-27 09:37:13