C014 The influence of rs3512 on miR-124–3p mediated regulation of FAN1 expression

<h3></h3> Huntington’s disease (HD) is an inherited neurodegenerative disorder caused by the expansion of CAG repeats. Genome-wide association studies using ENROLL-HD participants have identified age-at-onset modifiers that affect the CAG repeat instability in the Huntingtin gene based on its DNA repair function. One of the modifiers, FAN1, generates the strongest age-at-onset modification signals on chromosome 15 and its expression levels are inversely correlated with CAG repeat instability. More specifically, the various haplotypes of FAN1 are accountable for the two independent age-at-onset modifications. The missense mutations produced by rare variants lead to decreases in the DNA binding/nuclease activity of FAN1 and consequently hasten the age at onset. However, the mechanism for delayed onset by the most frequent haplotype is unclear. In this study, we show that binding a microRNA on 3’UTR SNP rs3512 mediates the most significant FAN1 eQTL signal and allelic imbalance in FAN1 mRNA related to the delayed onset haplotype. In particular, miR-124-3p binds preferentially on the reference allele at rs3512, inducing allelic imbalance, decreasing mRNA stability, and lowering FAN1 protein levels. Results of a further study on the miR-124-3p inhibitor using 3’UTR reporter assay with swap alleles support the effect of miR-124-3p on FAN1 level and the specificity of miR-124-3p at rs3512. Taken together, these results suggest that the rs3512 alternative allele is important for miR-124-3p mediated FAN1 level regulation, resulting in the delayed onset of increases in FAN1 levels and reducing CAG repeat instability.