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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 of alternative event regions with tDMR CpGs. *P < 10-5. A3SS, alternative 3’ splice site; A5SS, alternative 5’ splice site; ALE, alternative last exon; ATSS, alternative transcription start site; CE, cassette exon; CNE, constitutive exon; EI, exon isoforms; II, intron isoforms; IR, intron retention; MXE, mutually exclusive exon; tDMR, tissue-specific differentially methylated region.
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Figure 4: Enrichment of alternative event regions with tDMR CpGs. *P < 10-5. A3SS, alternative 3’ splice site; A5SS, alternative 5’ splice site; ALE, alternative last exon; ATSS, alternative transcription start site; CE, cassette exon; CNE, constitutive exon; EI, exon isoforms; II, intron isoforms; IR, intron retention; MXE, mutually exclusive exon; tDMR, tissue-specific differentially methylated region.

Mentions: It has been suggested that DNA methylation regulates alternative transcription [18], which may be the mechanism underlying its contribution to tissue-specific expression. In support of this hypothesis, we observed enrichment of tDMRs in alternative transcription start sites (ORP = 2.34, ORI = 2.58, P < 10-5; an example is given in Additional file 11: Figure S6; see also Additional file 5: Table S2). This was also reflected in the number of tDMRs associated with alternative transcription start sites (PT: 18.8%, IO: 20.9%). In addition, significant enrichment was observed at mutually exclusive exons (ORP = 1.47, ORI = 1.45, P < 10-5) and cassette exons (ORP = 1.37, ORI = 1.43, P < 10-5) (Figure 4). Overall, 47.9% of tDMRs detected in the peripheral tissue dataset and 49.8% of the tDMRs detected in the internal organ dataset mapped to an alternative transcription event. It was previously indicated that methylation of CGIs primarily mediates the effects on alternative transcription [10]. We could replicate the presence of a tDMR at a CGI in the SHANK3 gene body, which was found to regulate alternative transcription (Additional file 12: Figure S7) [10]. However, only a minority of tDMRs mapping to alternative transcription start sites (denoted by the occurrence of alternative first exons) were CGIs (PP = 14.5%; PI = 20.5%). The majority were non-CGI sequences (PP = 52.5%; PI = 48.3%) indicating a role for CpG-poor regions in the regulation of alternative transcription.


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 of alternative event regions with tDMR CpGs. *P < 10-5. A3SS, alternative 3’ splice site; A5SS, alternative 5’ splice site; ALE, alternative last exon; ATSS, alternative transcription start site; CE, cassette exon; CNE, constitutive exon; EI, exon isoforms; II, intron isoforms; IR, intron retention; MXE, mutually exclusive exon; 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 4: Enrichment of alternative event regions with tDMR CpGs. *P < 10-5. A3SS, alternative 3’ splice site; A5SS, alternative 5’ splice site; ALE, alternative last exon; ATSS, alternative transcription start site; CE, cassette exon; CNE, constitutive exon; EI, exon isoforms; II, intron isoforms; IR, intron retention; MXE, mutually exclusive exon; tDMR, tissue-specific differentially methylated region.
Mentions: It has been suggested that DNA methylation regulates alternative transcription [18], which may be the mechanism underlying its contribution to tissue-specific expression. In support of this hypothesis, we observed enrichment of tDMRs in alternative transcription start sites (ORP = 2.34, ORI = 2.58, P < 10-5; an example is given in Additional file 11: Figure S6; see also Additional file 5: Table S2). This was also reflected in the number of tDMRs associated with alternative transcription start sites (PT: 18.8%, IO: 20.9%). In addition, significant enrichment was observed at mutually exclusive exons (ORP = 1.47, ORI = 1.45, P < 10-5) and cassette exons (ORP = 1.37, ORI = 1.43, P < 10-5) (Figure 4). Overall, 47.9% of tDMRs detected in the peripheral tissue dataset and 49.8% of the tDMRs detected in the internal organ dataset mapped to an alternative transcription event. It was previously indicated that methylation of CGIs primarily mediates the effects on alternative transcription [10]. We could replicate the presence of a tDMR at a CGI in the SHANK3 gene body, which was found to regulate alternative transcription (Additional file 12: Figure S7) [10]. However, only a minority of tDMRs mapping to alternative transcription start sites (denoted by the occurrence of alternative first exons) were CGIs (PP = 14.5%; PI = 20.5%). The majority were non-CGI sequences (PP = 52.5%; PI = 48.3%) indicating a role for CpG-poor regions in the regulation of alternative transcription.

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