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dc.contributor.advisorBirney, Ewan
dc.contributor.authorTimmer, Sander Willem
dc.date.accessioned2015-02-05T11:52:00Z
dc.date.available2015-02-05T11:52:00Z
dc.date.issued2015-01-06
dc.identifier.otherPhD.38231
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/246693
dc.description.abstractGenetics has been successful in associating DNA sequence variants to both dichotomous and continuous traits in a variety of organisms, from plant and farm animal studies to human disease. With the advent of high-throughput genotyping, there has been an almost routine gen- eration of genome-wide association studies (GWAS) between human disease traits and genomic regions. Despite this success, a particular frustration is that the majority of associated loci are in non-coding regions of the genome and thus interpretation is hard. To improve characterisation of non-coding regions, molecular as- says can be used as a phenotype, and subsequently be used to explain how genetics alter molecular mechanisms. In this thesis, the inter- play of three molecular assays that are involved in regulating gene expression is studied. On 60 individuals, several assays are performed: FAIRE-chip, CTCF- seq, RNA-seq and DNA-seq. In the first part, the discovery and characteristics of FAIRE-QTLs is presented. The identified FAIRE-QTLs show strong overlap with other molecular QTLs, histone modifications, and transcription factors. The second part consists of the integration of genome-wide molecu- lar assays in a human population to reconstruct the human epigenome. Each of the molecular assays is associated with each of the other assays to discover phenotype-to-phenotype correlations. Furthermore, QTL data are used to dissect the causality for these phenotype-to-phenotype correlations in a system genetic manner. The third part presents a comprehensive view of CTCF binding on the X chromosome, and its implications for X-chromosome inactivation. A novel X chromosome-wide CTCF effect is observed. Using the gender of each of the cell lines, observations are made about which CTCF sites are dosage-compensated, active on both chromosomes, or are only bound in females.en
dc.language.isoenen
dc.rightsAttribution-NonCommercial-NoDerivs 2.0 UK: England & Wales*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/2.0/uk/*
dc.subjectgeneticsen
dc.subjectepigeneticsen
dc.subjectgwasen
dc.subjectdnaen
dc.subjectgene regulationen
dc.titleUnderstanding the epigenome using system geneticsen
dc.typeThesisen
dc.type.qualificationlevelDoctoral
dc.type.qualificationnameDoctor of Philosophy (PhD)
dc.publisher.institutionUniversity of Cambridgeen
dc.publisher.departmentEuropean Bioinformatics Instituteen
dc.publisher.departmentClare Hallen
dc.identifier.doi10.17863/CAM.15988


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Attribution-NonCommercial-NoDerivs 2.0 UK: England & Wales
Except where otherwise noted, this item's licence is described as Attribution-NonCommercial-NoDerivs 2.0 UK: England & Wales