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Fig. 3 | Clinical Epigenetics

Fig. 3

From: TREM2 upregulation correlates with 5-hydroxymethycytosine enrichment in Alzheimer’s disease hippocampus

Fig. 3

5-Hydroxymethylated DNA profiling in Alzheimer’s versus control hippocampus. a The figure shows the genomic locations of the amplicons (black bars) designed to assess the 5hmC enrichment at different regions of TREM2 by 5-hydroxymethylated DNA immunoprecipitation combined with RT-qPCR. UCSC Genes line denotes TREM2 gene predictions from the USCS track at the UCSC Genome Browser. hMeDIP-qPCR line shows the examined amplicons at the 3′ end of the gene (left), the gene body at exon 2 (middle), and the TSS-associated region (right). The GWAS SNP line shows the genomic position of the TREM2 variant (rs75932628) which is included in the amplicon at exon 2. b 5hMeDIP experiments, using an antibody against 5-hydroxymethylcytosine (5-hmC), revealed no differences in levels of 5-hydroymethylated DNA on the TSS-associated region (2.6-fold enrichment, p = 0.130) (left), and the gene body in exon 2 (1.5-fold enrichment, p = 0.383) (middle) and the 3′ end (1.7-fold enrichment, p = 0.633) (right) of TREM2 in the hippocampus samples of AD patients compared to controls. The graphs c and d show statistically significant positive correlation between 5hmC enrichment in the TREM2 exon2 region for the whole set of samples (c) and only for the AD-affected hippocampus (d)

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