Germline variants in UHRF1 are associated with multi-locus imprinting disturbance in humans and mice

A genetically engineered mouse model with a Uhrf1 p.(Lys661Asn) variant was developed. Mice homozygous for the variant born to healthy homozygous mothers displayed a range of phenotypes including prenatal lethality and multilocus imprinting disturbance was observed in affected mouse embryos. To determine if the embryonic lethality that was most pronounced at E17 might be a consequence of genomic methylation alterations present at an earlier stage of pregnancy, we undertook RRBS experiments on whole embryos at E11 from double homozygous crosses (n=10) and double wild type crosses (n=9). After filtering, 991,858 CpGs across the mouse genome were retained for the comparison of DNA methylation profiles between double homozygous crosses and double wild type crosses. The results revealed no significant alterations on DNA methylation between crosses with p-value adjusted < 0.05. Considering that whole embryos containing tissues with different DNA methylation profiles were analysed, we considered significant also those alterations with p-value unadjusted < 0.01, level change >10% and more than 1 CpG per region. Based on these criteria, we identified 11 CpG islands (all hypomethylated) that showed significant DNA methylation alterations between crosses at E11 (Supplementary Table 6). From these regions 10 out of 11 CpGi (Mcts2, Airn, Znf777, Znf444, Kcnq1ot1, Nnat, Zrsr1, Impact, Plagl1, Zfp787) were located within imprinted regions (Supplementary Table 6). The findings that E11 embryos born to homozygous Uhrf1 variant mothers showed frequent loss of methylation at iDMRs were further validated by pyrosequencing analysis (n=6 wild-type embyos; n=25 homozygous embryos) at Imprinted Control Regions (ICRs) (Figure 3E). This extendend analysis shows that embryos are variably and stochastically affected, with several embryos showing relative retention of DNA methylation at ICRs.