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Although Huntington’s disease (HD) is a well studied Mendelian genetic disorder, less is known about its associated epigenetic changes. Here, we characterize DNA methylation levels in six different tissues from 3 species: a mouse  huntingtin  (Htt) gene knock-in model, a transgenic  HTT  sheep model, and humans. Our epigenome-wide association study (EWAS) of human blood reveals that HD mutation status is significantly ( p  < 10 −7 ) associated with 33 CpG sites, including the  HTT  gene ( p  = 6.5 × 10 −26 ). These  Htt/HTT  associations were replicated in the Q175  Htt  knock-in mouse model ( p  = 6.0 × 10 −8 ) and in the transgenic sheep model ( p  = 2.4 × 10 −88 ). We define a measure of HD motor score progression among manifest HD cases based on multiple clinical assessments. EWAS of motor progression in manifest HD cases exhibits significant ( p  < 10 −7 ) associations with methylation levels at three loci: near  PEX14  ( p  = 9.3 × 10 −9 ),  GRIK4  ( p  = 3.0 × 10 −8 ), and  COX4I2  ( p  = 6.5 × 10 −8 ). We conclude that HD is accompanied by profound changes of DNA methylation levels in three mammalian species.

DNA methylation study of Huntington’s disease and motor progression in patients and in animal models