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Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation.

Paliwal A, Temkin AM, Kerkel K, Yale A, Yotova I, Drost N, Lax S, Nhan-Chang CL, Powell C, Borczuk A, Aviv A, Wapner R, Chen X, Nagy PL, Schork N, Do C, Torkamani A, Tycko B - PLoS Genet. (2013)

Bottom Line: Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb.Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR.Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, United States of America.

ABSTRACT
Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM.

Show MeSH
Local mapping of ASM in the CYP2A7 gene shows a discrete DMR that precisely overlaps a CTCF binding site.Bis-seq of heterozygous liver samples for multiple CYP2A7 amplicons shows ASM localized to a roughly 400 bp region (chr19: 41,386,227–41,386,613) spanning a CGI and a CTCF binding site in exon 2. ASM was evaluated visually and by a T-test on the percent methylation of individual clones, comparing the sets of clones for the two alleles.
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pgen-1003622-g007: Local mapping of ASM in the CYP2A7 gene shows a discrete DMR that precisely overlaps a CTCF binding site.Bis-seq of heterozygous liver samples for multiple CYP2A7 amplicons shows ASM localized to a roughly 400 bp region (chr19: 41,386,227–41,386,613) spanning a CGI and a CTCF binding site in exon 2. ASM was evaluated visually and by a T-test on the percent methylation of individual clones, comparing the sets of clones for the two alleles.

Mentions: Alignment of our methylation sequencing data with ChIP-Seq data from ENCODE and related projects, as displayed on the UCSC genome browser [14], showed that for both of the 2 imprinted domains, and for the non-imprinted STEAP3-C2orf76 intergenic region, though not for the ELK3 intragenic DMR, the DMRs with ASM overlapped precisely with empirically determined CTCF binding sites (Figs. 5, 6A and Figure S6). To ask whether there are additional examples of small discrete DMRs with strong and recurrent haplotype-dependent ASM that overlap with CTCF binding sites, we returned to an interesting locus with haplotype-dependent ASM and ASE that we had characterized in our initial report on this phenomenon [7], namely, the CYP2* gene cluster in chromosome band 19q13.2. As shown in Figure 7, the intragenic DMR in CYP2A7, tagged by SNP rs3815710, in fact shows discrete borders and precise co-localization with a CTCF binding site. Another DMR in this large gene cluster, tagged by SNP rs3844442 and located between 2 CYP2* pseudogenes [7], overlaps with a weaker CTCF binding site. Maps of each of these regions with haplotype-dependent ASM are shown aligned to haplotype blocks in Figure S7.


Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation.

Paliwal A, Temkin AM, Kerkel K, Yale A, Yotova I, Drost N, Lax S, Nhan-Chang CL, Powell C, Borczuk A, Aviv A, Wapner R, Chen X, Nagy PL, Schork N, Do C, Torkamani A, Tycko B - PLoS Genet. (2013)

Local mapping of ASM in the CYP2A7 gene shows a discrete DMR that precisely overlaps a CTCF binding site.Bis-seq of heterozygous liver samples for multiple CYP2A7 amplicons shows ASM localized to a roughly 400 bp region (chr19: 41,386,227–41,386,613) spanning a CGI and a CTCF binding site in exon 2. ASM was evaluated visually and by a T-test on the percent methylation of individual clones, comparing the sets of clones for the two alleles.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3757050&req=5

pgen-1003622-g007: Local mapping of ASM in the CYP2A7 gene shows a discrete DMR that precisely overlaps a CTCF binding site.Bis-seq of heterozygous liver samples for multiple CYP2A7 amplicons shows ASM localized to a roughly 400 bp region (chr19: 41,386,227–41,386,613) spanning a CGI and a CTCF binding site in exon 2. ASM was evaluated visually and by a T-test on the percent methylation of individual clones, comparing the sets of clones for the two alleles.
Mentions: Alignment of our methylation sequencing data with ChIP-Seq data from ENCODE and related projects, as displayed on the UCSC genome browser [14], showed that for both of the 2 imprinted domains, and for the non-imprinted STEAP3-C2orf76 intergenic region, though not for the ELK3 intragenic DMR, the DMRs with ASM overlapped precisely with empirically determined CTCF binding sites (Figs. 5, 6A and Figure S6). To ask whether there are additional examples of small discrete DMRs with strong and recurrent haplotype-dependent ASM that overlap with CTCF binding sites, we returned to an interesting locus with haplotype-dependent ASM and ASE that we had characterized in our initial report on this phenomenon [7], namely, the CYP2* gene cluster in chromosome band 19q13.2. As shown in Figure 7, the intragenic DMR in CYP2A7, tagged by SNP rs3815710, in fact shows discrete borders and precise co-localization with a CTCF binding site. Another DMR in this large gene cluster, tagged by SNP rs3844442 and located between 2 CYP2* pseudogenes [7], overlaps with a weaker CTCF binding site. Maps of each of these regions with haplotype-dependent ASM are shown aligned to haplotype blocks in Figure S7.

Bottom Line: Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb.Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR.Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, United States of America.

ABSTRACT
Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM.

Show MeSH