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Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array.

Slieker RC, Bos SD, Goeman JJ, Bovée JV, Talens RP, van der Breggen R, Suchiman HE, Lameijer EW, Putter H, van den Akker EB, Zhang Y, Jukema JW, Slagboom PE, Meulenbelt I, Heijmans BT - Epigenetics Chromatin (2013)

Bottom Line: Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation.Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons).We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands. B.T.Heijmans@lumc.nl.

ABSTRACT

Background: DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation. We used a new algorithm to identify and annotate tissue-specific differentially methylated regions (tDMRs) from Illumina 450k chip data for four peripheral tissues (blood, saliva, buccal swabs and hair follicles) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum and spleen with matched blood samples).

Results: The majority of tDMRs, in both relative and absolute terms, occurred in CpG-poor regions. Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons). Only a minority of tDMRs mapped to gene-body CpG islands (13%) or CpG islands shores (25%) suggesting a less prominent role for these regions than indicated previously. Implementation of ENCODE annotations showed enrichment of tDMRs in DNase hypersensitive sites and transcription factor binding sites. Despite the predominance of tissue differences, inter-individual differences in DNA methylation in internal tissues were correlated with those for blood for a subset of CpG sites in a locus- and tissue-specific manner.

Conclusions: We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription. Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that correlate to DNA methylation measured in easy accessible peripheral tissues.

No MeSH data available.


Related in: MedlinePlus

Within-individual correlation in DNA methylation between tissues. (A) Relation between differences within two individuals in blood versus one other tissue. (B) Venn diagram of the number of CpGs sites that are correlated between blood and one or more tissues. (C) Top: A variably methylated CpG site in muscle that is correlated with DNA methylation in blood. Bottom: A variably methylated CpG site that is correlated across all tissues likely due to the influence of SNPs. SC, subcutaneous; SNP, single nucleotide polymorphism.
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Figure 6: Within-individual correlation in DNA methylation between tissues. (A) Relation between differences within two individuals in blood versus one other tissue. (B) Venn diagram of the number of CpGs sites that are correlated between blood and one or more tissues. (C) Top: A variably methylated CpG site in muscle that is correlated with DNA methylation in blood. Bottom: A variably methylated CpG site that is correlated across all tissues likely due to the influence of SNPs. SC, subcutaneous; SNP, single nucleotide polymorphism.

Mentions: We investigated the occurrence of inter-individual variation in the internal tissue dataset after exclusion of CpG sites overlapping with known SNPs. Although tissue-differences were the main driver of variation in DNA methylation, we observed inter-individual variation for 15,803, 11,719, 46,437 and 8,415 CpGs in the liver, subcutaneous fat, omentum and skeletal muscle, respectively (defined as a mean sum of squares > 0.025). The large number of variable CpGs observed in omentum may reflect the cellular heterogeneity of this tissue. For the variable CpG sites identified, we calculated the correlation between the between-individual difference for the internal tissue and the between-individual difference for blood (Figure 6A). When restricting these CpG sites to those with a correlation >0.8, the within-individual DNA methylation in blood correlated to variable DNA methylation in the liver, subcutaneous fat, omentum and skeletal muscle for 5,532, 3,909, 10,905 and 2,446 CpGs, respectively. Many of the correlated CpG sites were unique for a single internal tissue and blood but others were correlated across multiple tissues (Figure 6B). While the former may represent a genuine epigenetic correlation, in particular CpGs correlating across all tissues may frequently be driven by genetic variation influencing local DNA methylation (Figure 6C).


Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array.

Slieker RC, Bos SD, Goeman JJ, Bovée JV, Talens RP, van der Breggen R, Suchiman HE, Lameijer EW, Putter H, van den Akker EB, Zhang Y, Jukema JW, Slagboom PE, Meulenbelt I, Heijmans BT - Epigenetics Chromatin (2013)

Within-individual correlation in DNA methylation between tissues. (A) Relation between differences within two individuals in blood versus one other tissue. (B) Venn diagram of the number of CpGs sites that are correlated between blood and one or more tissues. (C) Top: A variably methylated CpG site in muscle that is correlated with DNA methylation in blood. Bottom: A variably methylated CpG site that is correlated across all tissues likely due to the influence of SNPs. SC, subcutaneous; SNP, single nucleotide polymorphism.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750594&req=5

Figure 6: Within-individual correlation in DNA methylation between tissues. (A) Relation between differences within two individuals in blood versus one other tissue. (B) Venn diagram of the number of CpGs sites that are correlated between blood and one or more tissues. (C) Top: A variably methylated CpG site in muscle that is correlated with DNA methylation in blood. Bottom: A variably methylated CpG site that is correlated across all tissues likely due to the influence of SNPs. SC, subcutaneous; SNP, single nucleotide polymorphism.
Mentions: We investigated the occurrence of inter-individual variation in the internal tissue dataset after exclusion of CpG sites overlapping with known SNPs. Although tissue-differences were the main driver of variation in DNA methylation, we observed inter-individual variation for 15,803, 11,719, 46,437 and 8,415 CpGs in the liver, subcutaneous fat, omentum and skeletal muscle, respectively (defined as a mean sum of squares > 0.025). The large number of variable CpGs observed in omentum may reflect the cellular heterogeneity of this tissue. For the variable CpG sites identified, we calculated the correlation between the between-individual difference for the internal tissue and the between-individual difference for blood (Figure 6A). When restricting these CpG sites to those with a correlation >0.8, the within-individual DNA methylation in blood correlated to variable DNA methylation in the liver, subcutaneous fat, omentum and skeletal muscle for 5,532, 3,909, 10,905 and 2,446 CpGs, respectively. Many of the correlated CpG sites were unique for a single internal tissue and blood but others were correlated across multiple tissues (Figure 6B). While the former may represent a genuine epigenetic correlation, in particular CpGs correlating across all tissues may frequently be driven by genetic variation influencing local DNA methylation (Figure 6C).

Bottom Line: Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation.Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons).We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands. B.T.Heijmans@lumc.nl.

ABSTRACT

Background: DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation. We used a new algorithm to identify and annotate tissue-specific differentially methylated regions (tDMRs) from Illumina 450k chip data for four peripheral tissues (blood, saliva, buccal swabs and hair follicles) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum and spleen with matched blood samples).

Results: The majority of tDMRs, in both relative and absolute terms, occurred in CpG-poor regions. Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons). Only a minority of tDMRs mapped to gene-body CpG islands (13%) or CpG islands shores (25%) suggesting a less prominent role for these regions than indicated previously. Implementation of ENCODE annotations showed enrichment of tDMRs in DNase hypersensitive sites and transcription factor binding sites. Despite the predominance of tissue differences, inter-individual differences in DNA methylation in internal tissues were correlated with those for blood for a subset of CpG sites in a locus- and tissue-specific manner.

Conclusions: We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription. Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that correlate to DNA methylation measured in easy accessible peripheral tissues.

No MeSH data available.


Related in: MedlinePlus