PhD Defence: Gerard Arrey Tané

Title: The rebellious circles, Phenotypic consequences of circular DNAs in eukaryotic genomes

Supervisor: Birgitte Regenberg

Assessment committee:
Dr. Anton George Henssen
Dr. Jonathan Houseley
Chair: Vibe H. Oestergaard

The DNA in eukaryotes is organized inside the nucleus of the cell in discrete and linear molecules, the chromosomes. However, circular DNA molecules originating from the chromosomes lacking centromeres (extrachromosomal circular DNAs or eccDNAs) are increasingly being found in numerous eukaryotic species, showing that genomes are much more malleable than previously thought. While recent analysis have shown how ubiquitous and heterogeneous these molecules can be, tools and resources to model and study them have lacked.

This thesis aims to address basic biological questions of circular DNAs. In this thesis, I present a framework to approach circular DNA biology that accentuates formation, replication, segregation, elimination and selection as key features that determine circular DNA load in eukaryotic cells. Then, I present a method in which endogenous circular DNAs are produced in yeast using the Cre-LoxP system, which allow us to follow circular DNAs during growth of a cell population. With this method, I study the reintegration rate back into the linear chromosomes, showing how new alleles formed by circularization can be fixed. Overall, the project shows how circular DNAs are a source for genetic and phenotypic variability and how their integrations lead to more changes in the chromosomes. Here, I also introduce a circular DNA atlas across tissues and ages in mice. While much of the phenotypic effects of circular DNAs have been studied in the context of cancer, much of their effect in somatic healthy tissue has not been yet addressed. I isolated circular DNA from brain, muscle, liver, pancreas and adipose tissue from young (3-month-old), adult (12-month-old) and old (22-month-old) mice in order to study the effects of aging and tissue of origin. The study revealed genes being recurrently circularized, such as the olfactory receptor genes, as well as, tissue specific signatures, such as the Ugt1a genes in pancreas. 

The results of this thesis thus have implications in how we understand genetic plasticity during selective evolutionary processes and the genetic component of the aging process.