Fig. 3

Regional alterations in 5mC, 5hmC, and uC across adjacent sites are associated with AD neuropathology in the EC. a A differentially methylated region (DMR) was seen spanning two sites (cg05066959 and cg11823178) in the ANK1 gene. b Within the ARID5B gene, a DMR and a differentially unmodified cytosine region (DUR) were identified spanning the same six sites (cg00928816, cg07520810, cg14789659, cg16389209, cg16401465, and cg20746552). c One differentially hydroxymethylated region (DHR) was identified, residing within the FBXL16 gene and containing four CpG sites (cg01003448, cg01195246, cg02958327, cg07482202). An additional two DURs were also identified: d one residing within the JAG2 gene, which covered two loci (cg13617301 and cg19893664) and e another residing within the ALLC gene, also spanning two loci (cg04307702 and cg27089736). a–e Left panel shows box plot of adjusted beta value for individual loci making up the DMR, DHR, or DUR, adjusting for the co-variates of age, sex, and neuron/glia proportion, for individuals with low Braak stage (0–II) and high Braak stage (V–VI). Probes in a DMR are shown in purple, DHR in yellow, and DUR in gray. Right panel shows stack chart of differences in adjusted beta value averaged across all the probes in the region, after adjusting for the co-variates of age, sex, and neuron/glia proportion between individuals with low Braak stage (0–II) and high Braak stage (V–VI). 5mC levels are shown in purple, 5hmC levels are shown in yellow, and uC levels are shown in gray