Increased DNA Methylation at the AXIN1 Gene in a Monozygotic Twin from a Pair Discordant for a Caudal Duplication Anomaly N.A. Oates, J. van Vliet, D.L.

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Increased DNA Methylation at the AXIN1 Gene in a Monozygotic Twin from a Pair Discordant for a Caudal Duplication Anomaly N.A. Oates, J. van Vliet, D.L. Duffy, H.Y. Kroes, N.G. Martin, D.I. Boomsma, M. Campbell, M.G. Coulthard, E. Whitelaw, S. Chong The American Journal of Human Genetics Volume 79, Issue 1, Pages 155-162 (July 2006) DOI: 10.1086/505031 Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 1 AXIN1 CpG island methylation in the MZ twin pair (A, unaffected; B, affected) discordant for caudal duplication anomaly, their parents (D), and age- and sex-matched controls (C). An open circle represents an unmethylated CpG, a filled circle represents a methylated CpG, and each row of circles represents the methylation state of all 15 CpGs on a single allele. The square represents a SNP (G→T [dbSNPrs12928797]) commonly found in the samples analyzed. Overall percentage of methylation was calculated by determining the proportion of methylated CpGs relative to all CpGs. A detailed analysis of the methylation state at each CpG site is also shown (E). The American Journal of Human Genetics 2006 79, 155-162DOI: (10.1086/505031) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 2 Box-and-whisker plot of proportion-methylated CpG sites in the AXIN1 promoter per clone for each individual. Individuals are ordered by familial mean methylation level, with the index family at the top. Length of bar is interquartile range, and bar width is proportional to the number of clones analyzed for that individual. Solid diamonds are medians, and dashed lines extend to the observations 1.5× the interquartile range from the median, with open circles representing more-extreme values. The American Journal of Human Genetics 2006 79, 155-162DOI: (10.1086/505031) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 3 The degree of methylation of the AXIN1 promoter correlates with its activity in HEK 293 cells. A fragment of the AXIN1 locus, corresponding to nucleotides −416 to +114 relative to the start point of transcription (as determined by Evidence Viewer), was amplified by PCR from human genomic DNA (Promega). For a more detailed description of the methods used, see the main text. A similar trend was also seen in HeLa cells (data not shown). Each data point is the average of six replicates. Error bars represent two SDs. The American Journal of Human Genetics 2006 79, 155-162DOI: (10.1086/505031) Copyright © 2006 The American Society of Human Genetics Terms and Conditions

Figure 4 Quantification of X-chromosome inactivation in PBMCs by PCR amplification of the polymorphic human androgen-receptor (HUMARA) locus after digestion with RsaI or RsaI and HpaII. Although the pair both display some skewing towards the larger allele, the pattern is highly consistent in both twins. The American Journal of Human Genetics 2006 79, 155-162DOI: (10.1086/505031) Copyright © 2006 The American Society of Human Genetics Terms and Conditions