Hypermethylation of the CpG Island Near the G4C2 Repeat in ALS with a C9orf72 Expansion Zhengrui Xi, Lorne Zinman, Danielle Moreno, Jennifer Schymick,

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Hypermethylation of the CpG Island Near the G4C2 Repeat in ALS with a C9orf72 Expansion Zhengrui Xi, Lorne Zinman, Danielle Moreno, Jennifer Schymick, Yan Liang, Christine Sato, Yonglan Zheng, Mahdi Ghani, Samar Dib, Julia Keith, Janice Robertson, Ekaterina Rogaeva The American Journal of Human Genetics Volume 92, Issue 6, Pages 981-989 (June 2013) DOI: 10.1016/j.ajhg.2013.04.017 Copyright © 2013 The American Society of Human Genetics Terms and Conditions

Figure 1 HhaI Assay (A) A schematic presentation of the genomic region around the G4C2 repeat. Two predicted CpG islands located in the sequences flanking the repeat were covered by three fragments. (B) DNA undigested and digested with HhaI was amplified for all three fragments and the resulting band intensity quantified. Only fragment #1 shows differential methylation between expansion carriers and noncarriers. (C) Samples with intermediate size alleles (24–43 repeats) were not methylated upstream of the G4C2 repeat (fragment #1). (D) Representative gel analysis of 12 ALS expansion carriers, 12 ALS noncarriers, and 12 controls (a higher methylation level was observed in expansion carriers versus noncarriers). The American Journal of Human Genetics 2013 92, 981-989DOI: (10.1016/j.ajhg.2013.04.017) Copyright © 2013 The American Society of Human Genetics Terms and Conditions

Figure 2 Correlation between HhaI Assay and the Bisulfite Sequencing Assay (A) Representative chromatograms of a sequence containing seven CpG sites for an expansion carrier and a noncarrier. (B) A scatter plot of the observed methylation ratio (HhaI assay) and number of methylated CpG sites (bisulfite sequencing) revealed a significant correlation between the two assays with blood DNA. The American Journal of Human Genetics 2013 92, 981-989DOI: (10.1016/j.ajhg.2013.04.017) Copyright © 2013 The American Society of Human Genetics Terms and Conditions

Figure 3 Methylation Results in Three Representative Families of Probands who Carry the C9orf72 Expansion All available family members were studied to compare methylation levels. Individual ID and C9orf72 genotype are shown beneath the corresponding diamond. Arabic numbers indicate the repeat number and “exp” represents the expansion allele. Age at the time of examination is shown in the upper right corner. Age of onset is indicated above the ID number. Gender of the family members is masked to protect confidentiality. Black/white inverted gel images from the HhaI assay are shown below the genotype. The individual number of methylated CpG sites is shown on the right side of the gel image beneath “BSP,” which stands for bisulfite sequencing PCR. The American Journal of Human Genetics 2013 92, 981-989DOI: (10.1016/j.ajhg.2013.04.017) Copyright © 2013 The American Society of Human Genetics Terms and Conditions

Figure 4 Relative Quantification of C9orf72 mRNA All transcripts were detected by an inventoried TaqMan gene expression assay (Hs00376619_m1) and relative expression was obtained by normalizing to three reference genes (HPRT1, UBC, and B2M). Error bars represent the standard error of the triplicate reactions. Expansion carriers were shown to have reduced C9orf72 expression compared nonexpansion carriers, whereas ID #8520 with 43 repeats had a normal C9orf72 mRNA level. Notably, gene expression is inversely related to methylation level. Number of methylated CpG site is shown beneath each sample. “BSP” stands for bisulfite sequencing PCR. The American Journal of Human Genetics 2013 92, 981-989DOI: (10.1016/j.ajhg.2013.04.017) Copyright © 2013 The American Society of Human Genetics Terms and Conditions