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Non-imprinted allele-specific DNA methylation on human autosomes.

Zhang Y, Rohde C, Reinhardt R, Voelcker-Rehage C, Jeltsch A - Genome Biol. (2009)

Bottom Line: Based on our results, allele-specific methylation is likely to affect about 10% of all human genes and to contribute to allele-specific expression and monoallelic gene silencing.In most cases, we observed that some, but not all, heterozygous individuals showed allele-specific methylation, suggesting that allele-specific methylation is the outcome of an epigenetic drift, the direction of which is determined by the genetic differences between the alleles.Therefore, genetic differences must be taken into account in future comparative DNA methylation studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany. y.zhang@jacobs-university.de

ABSTRACT

Background: Differential DNA methylation between alleles is well established in imprinted genes and the X chromosomes in females but has rarely been reported at non-imprinted loci on autosomes.

Results: We studied DNA methylation of cytosine-guanine dinucleotide (CpG) islands on chromosome 21 in leukocytes from several healthy individuals and observed novel cases of pronounced differential methylation of alleles. Allele-specific methylation affected complete CpG islands with methylation differences between alleles of up to 85%. The methylation differences between alleles were strongly correlated with the genotypes, excluding a connection to imprinting. We show that allele-specific methylation can lead to allelic repression of the methylated gene copy. Based on our results, allele-specific methylation is likely to affect about 10% of all human genes and to contribute to allele-specific expression and monoallelic gene silencing. Therefore, allele-specific methylation represents an epigenetic pathway of how genetic polymorphisms may lead to phenotypic variability. In most cases, we observed that some, but not all, heterozygous individuals showed allele-specific methylation, suggesting that allele-specific methylation is the outcome of an epigenetic drift, the direction of which is determined by the genetic differences between the alleles. We could show that the tendency to acquire hypermethylation in one allele was inherited.

Conclusions: We observed that larger differences in methylation levels between individuals were often coupled to allele-specific methylation and genetic polymorphisms, suggesting that the inter-individual variability of DNA methylation is strongly influenced by genetic differences. Therefore, genetic differences must be taken into account in future comparative DNA methylation studies.

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Allele-specific methylation and expression of amplicons 23_1 and 23_2. (a) Example of ASM of amplicons 23_1 and 23_2 in the first exon of gene C21orf81. The figure shows the position of these two amplicons in the UCSC genome browser and the methylation pattern of alleles in both amplicons. Each row corresponds to one clone of bisulfite PCR products. Each column corresponds to one CpG site in the studied region. The color code indicates different methylation states of the CpG sites (blue, unmethylated; red, methylated; white, methylation state unknown). The clones in each amplicon were sorted according to their genotype at two SNPs (dbsnp rs56270809 on 23_2 and dbsnp rs2297246 on 23_1), the positions of which are indicated by an arrow. By sequencing of the genomic DNA we identified the haplotype of all samples with ASM to be either A/A or C/C as schematically shown in the lower part of the figure. Expression analysis showed that the gene is exclusively expressed from the unmethylated A allele (indicated by an asterisk) in leukocytes (data are shown from individual 11). (b) Compilation of results from all heterozygous individuals in amplicon 23_1. The individuals were sorted according to the decreasing methylation difference between alleles. Each row corresponds to a single allele from one individual. Each square represents the average methylation of a CpG site encoded in a continuous yellow to blue color code. The original methylation patterns of all samples with ASM are shown in Additional file 4. (c) Methylation level of each allele from all heterozygous individuals in amplicon 23_1. (d) Compilation of results from all heterozygous individuals in amplicon 23_2. The original methylation patterns of all samples with ASM are shown in Additional file 4. (e) Methylation level of each allele from all heterozygous individuals in amplicon 23_2.
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Figure 2: Allele-specific methylation and expression of amplicons 23_1 and 23_2. (a) Example of ASM of amplicons 23_1 and 23_2 in the first exon of gene C21orf81. The figure shows the position of these two amplicons in the UCSC genome browser and the methylation pattern of alleles in both amplicons. Each row corresponds to one clone of bisulfite PCR products. Each column corresponds to one CpG site in the studied region. The color code indicates different methylation states of the CpG sites (blue, unmethylated; red, methylated; white, methylation state unknown). The clones in each amplicon were sorted according to their genotype at two SNPs (dbsnp rs56270809 on 23_2 and dbsnp rs2297246 on 23_1), the positions of which are indicated by an arrow. By sequencing of the genomic DNA we identified the haplotype of all samples with ASM to be either A/A or C/C as schematically shown in the lower part of the figure. Expression analysis showed that the gene is exclusively expressed from the unmethylated A allele (indicated by an asterisk) in leukocytes (data are shown from individual 11). (b) Compilation of results from all heterozygous individuals in amplicon 23_1. The individuals were sorted according to the decreasing methylation difference between alleles. Each row corresponds to a single allele from one individual. Each square represents the average methylation of a CpG site encoded in a continuous yellow to blue color code. The original methylation patterns of all samples with ASM are shown in Additional file 4. (c) Methylation level of each allele from all heterozygous individuals in amplicon 23_1. (d) Compilation of results from all heterozygous individuals in amplicon 23_2. The original methylation patterns of all samples with ASM are shown in Additional file 4. (e) Methylation level of each allele from all heterozygous individuals in amplicon 23_2.

Mentions: We observed strong ASM on the first exon of the C21orf81 gene where we studied the methylation pattern of amplicon 23_2 and 23_1, which are located next to each other and cover almost the entire CpG island (Figure 2a). The analysis for amplicon 23_1 was performed in 38 individuals, 17 of which had an A/C SNP in the sequenced region. Out of them, we observed ASM with a methylation difference of >30% in eight cases, always having the A allele hypomethylated (Table 1; Figure 2; Additional file 4). Some individuals showed a weaker DNA methylation difference between alleles, and in other cases no DNA methylation difference was detectable. Within the 21 homozygous individuals, we observed a biphasic distribution of DNA methylation levels in 9 cases, suggesting the potential presence of ASM, although this could not be identified because of the lack of a characteristic SNP.


Non-imprinted allele-specific DNA methylation on human autosomes.

Zhang Y, Rohde C, Reinhardt R, Voelcker-Rehage C, Jeltsch A - Genome Biol. (2009)

Allele-specific methylation and expression of amplicons 23_1 and 23_2. (a) Example of ASM of amplicons 23_1 and 23_2 in the first exon of gene C21orf81. The figure shows the position of these two amplicons in the UCSC genome browser and the methylation pattern of alleles in both amplicons. Each row corresponds to one clone of bisulfite PCR products. Each column corresponds to one CpG site in the studied region. The color code indicates different methylation states of the CpG sites (blue, unmethylated; red, methylated; white, methylation state unknown). The clones in each amplicon were sorted according to their genotype at two SNPs (dbsnp rs56270809 on 23_2 and dbsnp rs2297246 on 23_1), the positions of which are indicated by an arrow. By sequencing of the genomic DNA we identified the haplotype of all samples with ASM to be either A/A or C/C as schematically shown in the lower part of the figure. Expression analysis showed that the gene is exclusively expressed from the unmethylated A allele (indicated by an asterisk) in leukocytes (data are shown from individual 11). (b) Compilation of results from all heterozygous individuals in amplicon 23_1. The individuals were sorted according to the decreasing methylation difference between alleles. Each row corresponds to a single allele from one individual. Each square represents the average methylation of a CpG site encoded in a continuous yellow to blue color code. The original methylation patterns of all samples with ASM are shown in Additional file 4. (c) Methylation level of each allele from all heterozygous individuals in amplicon 23_1. (d) Compilation of results from all heterozygous individuals in amplicon 23_2. The original methylation patterns of all samples with ASM are shown in Additional file 4. (e) Methylation level of each allele from all heterozygous individuals in amplicon 23_2.
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Related In: Results  -  Collection

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Show All Figures
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Figure 2: Allele-specific methylation and expression of amplicons 23_1 and 23_2. (a) Example of ASM of amplicons 23_1 and 23_2 in the first exon of gene C21orf81. The figure shows the position of these two amplicons in the UCSC genome browser and the methylation pattern of alleles in both amplicons. Each row corresponds to one clone of bisulfite PCR products. Each column corresponds to one CpG site in the studied region. The color code indicates different methylation states of the CpG sites (blue, unmethylated; red, methylated; white, methylation state unknown). The clones in each amplicon were sorted according to their genotype at two SNPs (dbsnp rs56270809 on 23_2 and dbsnp rs2297246 on 23_1), the positions of which are indicated by an arrow. By sequencing of the genomic DNA we identified the haplotype of all samples with ASM to be either A/A or C/C as schematically shown in the lower part of the figure. Expression analysis showed that the gene is exclusively expressed from the unmethylated A allele (indicated by an asterisk) in leukocytes (data are shown from individual 11). (b) Compilation of results from all heterozygous individuals in amplicon 23_1. The individuals were sorted according to the decreasing methylation difference between alleles. Each row corresponds to a single allele from one individual. Each square represents the average methylation of a CpG site encoded in a continuous yellow to blue color code. The original methylation patterns of all samples with ASM are shown in Additional file 4. (c) Methylation level of each allele from all heterozygous individuals in amplicon 23_1. (d) Compilation of results from all heterozygous individuals in amplicon 23_2. The original methylation patterns of all samples with ASM are shown in Additional file 4. (e) Methylation level of each allele from all heterozygous individuals in amplicon 23_2.
Mentions: We observed strong ASM on the first exon of the C21orf81 gene where we studied the methylation pattern of amplicon 23_2 and 23_1, which are located next to each other and cover almost the entire CpG island (Figure 2a). The analysis for amplicon 23_1 was performed in 38 individuals, 17 of which had an A/C SNP in the sequenced region. Out of them, we observed ASM with a methylation difference of >30% in eight cases, always having the A allele hypomethylated (Table 1; Figure 2; Additional file 4). Some individuals showed a weaker DNA methylation difference between alleles, and in other cases no DNA methylation difference was detectable. Within the 21 homozygous individuals, we observed a biphasic distribution of DNA methylation levels in 9 cases, suggesting the potential presence of ASM, although this could not be identified because of the lack of a characteristic SNP.

Bottom Line: Based on our results, allele-specific methylation is likely to affect about 10% of all human genes and to contribute to allele-specific expression and monoallelic gene silencing.In most cases, we observed that some, but not all, heterozygous individuals showed allele-specific methylation, suggesting that allele-specific methylation is the outcome of an epigenetic drift, the direction of which is determined by the genetic differences between the alleles.Therefore, genetic differences must be taken into account in future comparative DNA methylation studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany. y.zhang@jacobs-university.de

ABSTRACT

Background: Differential DNA methylation between alleles is well established in imprinted genes and the X chromosomes in females but has rarely been reported at non-imprinted loci on autosomes.

Results: We studied DNA methylation of cytosine-guanine dinucleotide (CpG) islands on chromosome 21 in leukocytes from several healthy individuals and observed novel cases of pronounced differential methylation of alleles. Allele-specific methylation affected complete CpG islands with methylation differences between alleles of up to 85%. The methylation differences between alleles were strongly correlated with the genotypes, excluding a connection to imprinting. We show that allele-specific methylation can lead to allelic repression of the methylated gene copy. Based on our results, allele-specific methylation is likely to affect about 10% of all human genes and to contribute to allele-specific expression and monoallelic gene silencing. Therefore, allele-specific methylation represents an epigenetic pathway of how genetic polymorphisms may lead to phenotypic variability. In most cases, we observed that some, but not all, heterozygous individuals showed allele-specific methylation, suggesting that allele-specific methylation is the outcome of an epigenetic drift, the direction of which is determined by the genetic differences between the alleles. We could show that the tendency to acquire hypermethylation in one allele was inherited.

Conclusions: We observed that larger differences in methylation levels between individuals were often coupled to allele-specific methylation and genetic polymorphisms, suggesting that the inter-individual variability of DNA methylation is strongly influenced by genetic differences. Therefore, genetic differences must be taken into account in future comparative DNA methylation studies.

Show MeSH