Fewings, N. | Search bioRxiv

bioRxiv2020

LINE-1 DNA methylation in response to aging and vitamin D

Retrotransposons are genetic elements capable of their own propagation and insertion into the human genome. Because of their mutagenic potential, retrotransposons are heavily suppressed by mechanisms including DNA methylation. Increased age is associated with decreasing DNA methylation of the LINE-1 retrotransposon and may partially explain the predisposition towards malignancy with advancing age. Vitamin D has been investigated for its effects on DNA methylation at LINE-1 elements with mixed results. This study hypothesised that LINE-1 DNA methylation is altered by vitamin D exposure and age. Using whole genome bisulfite sequencing of adult and newborn haematopoietic progenitors, DNA methylation at LINE-1 elements was not found to vary between cells cultured with or without calcitriol, both in adults and newborns. In contrast, several LINE-1 regions were found to be differentially methylated between adults and children, but these were not uniformly hypermethylated in paediatric cells. The results of this study suggest that at least in haematopoietic cells, vitamin D does not appear to affect LINE-1 methylation.

genetics↗

bioRxiv2018

Genetic evidence that the latency III stage of Epstein-Barr Virus infection is a therapeutic target for Multiple Sclerosis

Genome wide association studies have identified >200 susceptibility loci accounting for much of the heritability of Multiple Sclerosis (MS). Epstein Barr virus (EBV), a memory B cell tropic virus, has been identified as necessary but not sufficient for development of MS, with evidence for disease causation. The molecular and immunological basis for this has not been established. LCL proliferation is driven by signalling through the EBV produced cell surface protein LMP1, a homologue of the MS risk gene CD40. We show that the CD40 ligand, CD40L, potentially through competitive signalling with LMP1, reduces LCL proliferation (p<0.001). The MS risk variants of the LMP1 signalling inhibitor, TRAF3, had altered expression in B cells and LCLs. Both CD40 and TRAF3 risk SNPs are in binding sites for the EBV transcription factor EBNA2. We have investigated transcriptomes of B cells and EBV infected B cells at Latency III (LCLs) and identified 47 MS risk genes with altered expression, associated with the risk genotype. Overall these MS risk SNPs were overrepresented in target loci of the EBV transcription factor EBNA2 (p<10-16), in genes dysregulated between B and LCLs (p<10-5), and as targets for EBV miRNAs (p<10-4). The risk gene ZC3HAV1 is the putative target for multiple EBV miRNAs. It amplifies the interferon response, and was shown to have reduced expression in LCLs for the risk allele. These data indicate targeting EBV EBNA2, miRNAs, and MS risk genes on the LMP1/LMP2 pathways, and the pathways themselves, may be of therapeutic benefit in MS.

genomics↗