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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

Enrichment with tDMRs in the gene- and CpG-density centric annotation. Differences were observed between CGI and non-CGI regions, especially in proximal promoters and downstream regions. Shores in distal promoters and downstream regions were enriched with tDMR CpGs. Enrichment with tDMR CpGs in non-CGI features was limited to distal promoters and proximal promoters. * P < 10-5. CGI, CpG island; tDMR, tissue-specific differentially methylated region.
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Figure 2: Enrichment with tDMRs in the gene- and CpG-density centric annotation. Differences were observed between CGI and non-CGI regions, especially in proximal promoters and downstream regions. Shores in distal promoters and downstream regions were enriched with tDMR CpGs. Enrichment with tDMR CpGs in non-CGI features was limited to distal promoters and proximal promoters. * P < 10-5. CGI, CpG island; tDMR, tissue-specific differentially methylated region.

Mentions: In order to systematically assess previous observations regarding tDMR annotations and to further explore annotations that became available more recently, we created extensive annotations of CpG sites interrogated with the 450k chip (the annotations can be found in Additional file 8) and evaluated their enrichment in tDMRs. First, tDMR CpGs were annotated according to the location relative to genes. This showed that the occurrence of tDMRs in proximal promoters (defined as −1500 to +500 from a TSS) was depleted, whereas it was enriched in other gene-centric annotations (Additional file 9: Figure S5). This pattern was highly concordant between internal and peripheral tissues (for example, for proximal promoters ORP = 0.70 and ORI = 0.68, P < 10-5). Next, we combined the gene-centric annotation with a CGI-centric annotation (Figure 2). The combined annotation revealed that the overall depletion in proximal promoters was due to a strong underrepresentation of tDMRs in CGI proximal promoters (Figure 2, ORP = 0.15, ORI = 0.19, P < 10-5). Conversely, non-CGI proximal promoters were strongly enriched for differential methylation (ORP = 3.10, ORI = 2.83, P < 10-5). Also in absolute terms, more tDMRs mapped to non-CGI proximal promoters (nP = 781, nI = 1,100) than CGI proximal promoters (nP = 168, nI = 313; Additional file 10: Table S3 and Additional file 5: Table S2). In proximal promoters, no enrichment of CGI shores was observed (ORP = 0.82, ORI = 0.80), while CGI shelves (that is, a 2 kb region flanking a CGI shore) showed a similar enrichment compared to the non-CGI proximal promoters (ORP = 3.10, ORI = 3.10, P < 10-5). In accordance with the preferential occurrence of tDMRs at non-CGI proximal promoters, the genes adjacent to these tDMRs were strongly enriched for tissue-specific gene expression, much more so than for CGI proximal promoters (Figure 3).


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)

Enrichment with tDMRs in the gene- and CpG-density centric annotation. Differences were observed between CGI and non-CGI regions, especially in proximal promoters and downstream regions. Shores in distal promoters and downstream regions were enriched with tDMR CpGs. Enrichment with tDMR CpGs in non-CGI features was limited to distal promoters and proximal promoters. * P < 10-5. CGI, CpG island; tDMR, tissue-specific differentially methylated region.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Enrichment with tDMRs in the gene- and CpG-density centric annotation. Differences were observed between CGI and non-CGI regions, especially in proximal promoters and downstream regions. Shores in distal promoters and downstream regions were enriched with tDMR CpGs. Enrichment with tDMR CpGs in non-CGI features was limited to distal promoters and proximal promoters. * P < 10-5. CGI, CpG island; tDMR, tissue-specific differentially methylated region.
Mentions: In order to systematically assess previous observations regarding tDMR annotations and to further explore annotations that became available more recently, we created extensive annotations of CpG sites interrogated with the 450k chip (the annotations can be found in Additional file 8) and evaluated their enrichment in tDMRs. First, tDMR CpGs were annotated according to the location relative to genes. This showed that the occurrence of tDMRs in proximal promoters (defined as −1500 to +500 from a TSS) was depleted, whereas it was enriched in other gene-centric annotations (Additional file 9: Figure S5). This pattern was highly concordant between internal and peripheral tissues (for example, for proximal promoters ORP = 0.70 and ORI = 0.68, P < 10-5). Next, we combined the gene-centric annotation with a CGI-centric annotation (Figure 2). The combined annotation revealed that the overall depletion in proximal promoters was due to a strong underrepresentation of tDMRs in CGI proximal promoters (Figure 2, ORP = 0.15, ORI = 0.19, P < 10-5). Conversely, non-CGI proximal promoters were strongly enriched for differential methylation (ORP = 3.10, ORI = 2.83, P < 10-5). Also in absolute terms, more tDMRs mapped to non-CGI proximal promoters (nP = 781, nI = 1,100) than CGI proximal promoters (nP = 168, nI = 313; Additional file 10: Table S3 and Additional file 5: Table S2). In proximal promoters, no enrichment of CGI shores was observed (ORP = 0.82, ORI = 0.80), while CGI shelves (that is, a 2 kb region flanking a CGI shore) showed a similar enrichment compared to the non-CGI proximal promoters (ORP = 3.10, ORI = 3.10, P < 10-5). In accordance with the preferential occurrence of tDMRs at non-CGI proximal promoters, the genes adjacent to these tDMRs were strongly enriched for tissue-specific gene expression, much more so than for CGI proximal promoters (Figure 3).

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