Variable methylation of endogenous retroviruses: epigenetic inheritance, environmental modulation, and genetic modifiers

Half of the mammalian genome is made up of transposable elements (TEs), the vast majority of which are modified by DNA methylation and repressive histone marks. Intracisternal A-particles (IAPs) are evolutionarily young murine-specific endogenous retroviruses (ERVs). Some are capable of retrotransposition and many harbour regulatory sequences with the potential to influence host gene expression. Previous work has shown that, at the Agouti Viable Yellow (Avy) locus, an IAP insertion provides an alternative promoter for the Agouti coat colour gene. Variable methylation of this IAP is correlated with coat colour expressivity. In addition, the Avy allele exhibits transgenerational epigenetic inheritance, susceptibility to environmental exposures, and strain-specific modulation. A recent screen conducted in the C57BL/6J mouse strain identified a subset of IAPs that show variable methylation levels across genetically identical individuals. This thesis characterises this novel repertoire of variably methylated IAPs (VM-IAPs) and in doing so assesses the extent to which endogenous retroviruses in the mammalian genome display Avy-like properties. Findings indicate that VM-IAPs become hypermethylated in the male germline by the DNA methyltransferase DNMT3C and are reconstructed as variable loci in the next generation. An exploration of inter-individual VM-IAP methylation levels in the C57BL/6J population demonstrates that their frequency distributions form skewed bell curves that are locus-specific. Only one out of six VM-IAPs analysed via linear mixed effects models shows memory of maternal methylation level, and the effect size is small. This challenges the generalisability of epigenetic inheritance at these regions. In studying environmental influences on VM-IAPs, results suggest that these epigenetically dynamic loci are selectively susceptible to altered environmental conditions: abnormal folate metabolism appears to shift VM-IAP methylation levels and influence VM-IAP-associated gene expression, while no significant effects are observed following exposure to the endocrine-disruptor Bisphenol-A (BPA) or to an obesogenic diet. A longitudinal ageing analysis indicates that VM-IAPs are stable across the murine lifespan, with only modest increases in methylation detected for a subset of loci. Reciprocal hybrid breeding experiments reveal that VM-IAP methylation levels are subject to maternal and genetic background effects that can be harnessed to map strain-specific VM IAP modifiers. Finally, a naturally occurring genetically-conferred epiallele that influences neighbouring gene expression is identified and characterised. This body of work highlights the value of using VM-IAPs as a model to study TE regulation and mammalian epigenetic stochasticity, and serves as a foundation to elucidate the consequences of partially methylated repeat elements on genome structure and function.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2020

Author dc:creator

• Bertozzi, Tessa Mariah

Advisor dc:contributor.advisor

• Ferguson-Smith, Anne

• DNA methylation
• metastable epiallele
• epigenetic inheritance
• endogenous retrovirus
• IAP

Licence

• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/55113d3c-355b-400d-8659-3a11036b8440/download
• https://www.rioxx.net/licenses/all-rights-reserved/

Language dc:language

en

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.50189

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/303113