Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array
- Roderick C Slieker1,
- Steffan D Bos1, 2,
- Jelle J Goeman3,
- Judith VMG Bovée4,
- Rudolf P Talens1,
- Ruud van der Breggen1,
- H Eka D Suchiman1,
- Eric-Wubbo Lameijer1,
- Hein Putter3,
- Erik B van den Akker1, 5,
- Yanju Zhang1,
- J Wouter Jukema6,
- P Eline Slagboom1, 2,
- Ingrid Meulenbelt1, 2 and
- Bastiaan T Heijmans1, 2Email author
© Slieker et al.; licensee BioMed Central Ltd. 2013
Received: 8 May 2013
Accepted: 28 June 2013
Published: 6 August 2013
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).
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.
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.
KeywordsDifferentially methylated region Illumina 450k Annotation Algorithm Tissue
Epigenetic mechanisms, including DNA methylation, are essential in mammalian development and cell differentiation . Several studies have compared genome-wide DNA methylation patterns, particularly of cytosine at CpG dinucleotides, between human cell types and tissues to identify general characteristics of genomic regions that define epigenetic differences between tissues [2–4]. However, these studies often focused on a subset of regions either because of a priori hypotheses or due to the limited coverage of the DNA methylation profiling technology used. For example, while many studies have explored and identified tissue-specific differentially methylated regions (tDMRs) at promoter sequences [2, 4–8], differential methylation at other genomic regions has been investigated less widely and consistently. Several studies focussed on CpG islands (CGIs), which are genomic regions with a high density of CpGs, and reported the predominant occurrence of tDMR CGIs located in the gene bodies [9–11] and described their potential role in regulating alternative transcription start sites . One study highlighted the 2 kb region flanking CGIs (that is, CGI shores) as a frequent target of tissue-specific methylation , but this finding was not replicated in a mouse study .
To study the contribution of epigenetic variation to human disease risk, it is necessary not only to study tissue differences, but also to explore the correlation of DNA methylation signatures between tissues. Many diseases involve internal organs (IOs) that cannot be sampled in human subjects participating in epidemiological studies. Studies of such diseases would be facilitated if methylation of DNA from peripheral tissues could be used as a proxy; that is, if inter-individual variation in DNA methylation levels at a genomic region that is observed in a population is positively correlated with that in an (unmeasured) internal organ. Although candidate region  and genome-wide  studies suggested that correlated DNA methylation across tissues may occur, little is known about the prevalence of such correlations.
In this study, we explored genome-wide DNA methylation in six internal and four peripheral tissues in two independent datasets using the Illumina 450k methylation chip [14, 15]. Apart from systematically covering promoter regions, CGIs and CGI shores, the chip targets sufficient CpG dinucleotides outside these regions to study other annotations. We implemented an algorithm to identify tDMRs, which allowed us to detect statistically robust and biologically relevant tDMRs in 450k data. This allowed us to evaluate previously indicated annotations of tDMRs systematically in a single study. In addition, we explored annotations utilizing more recent insights on genome biology including those from the ENCODE project. Finally, we evaluated the occurrence of correlated DNA methylation across tissues.
Identification of tDMRs
Genome-wide DNA methylation data was generated from four peripheral tissues (blood, saliva, hair follicles and buccal swabs) from five individuals, and six internal tissues (subcutaneous fat, omentum, muscle, liver, spleen and pancreas) and blood from six individuals, using Illumina 450k DNA methylation chips (Additional file 1: Table S1). The DNA methylation patterns observed in the tissues were in concordance with previously described characteristics: the distribution of DNA methylation was bimodal with a minority of CG dinucleotides showing intermediate DNA methylation levels (Additional file 2: Figure S1A, B); the canonical pattern of low DNA methylation around transcription start sites (TSSs) was observed (Additional file 3: Figure S2A); and, finally, adjacent CpGs within 1 kb had similar DNA methylation levels (Additional file 3: Figure S2B).
Characteristics of identified tDMRs
Number of DMR
Number of CpGs
Mean length (SD)
Median length (IQR)
Unique between datasets
Shared between datasets
tDMRs accumulate near genes expressed in specific tissues
tDMRs were mapped to their nearest gene and the TiGER database was used to verify the expectation that these genes are preferentially expressed in investigated tissues . This was indeed the case (Additional file 7: Figure S4A, Additional file 5: Table S2). For example, tDMRs in the internal tissue dataset mapped preferentially to liver-specific genes (odds ratio for internal organs ORI = 5.01, P < 10-5). In contrast, this was not observed in the peripheral tissue dataset (odds ratio for peripheral tissues ORP = 1.02, P = 0.13). Enrichment of the blood-specific expression of genes adjacent to identified tDMRs was observed in both datasets (ORP = 2.42, P < 10-5; ORI = 1.88, P < 10-5). Furthermore, tDMRs mapping to genes with tissue-specific expression were hypomethylated in the tissue in which the gene is preferentially expressed compared with other tissues. This is in line with an inverse relationship between DNA methylation and expression (Additional file 7: Figure S4B). Taken together, these analyses indicate that our algorithm detected a tDMR set that is not only statistically robust but also biologically relevant.
tDMRs associate with specific genomic annotations
Other regions showing evidence for enrichment for tissue-specific methylation included CGIs in downstream regions (defined as the 3’ end to +5 kb relative to the 3’ end; ORP = 1.46, P = 0.017; ORI = 1.76, P < 10-5), CGI shores in distal promoters (ORP = 1.59, ORI = 1.78, P < 10-5) and CGI shores in downstream regions (ORP = 1.67, P = 4 × 10-4; ORI = 1.58, P = 1.2 × 10-4). Of note, no enrichment was observed for gene-body CGIs (defined as +500 kb to the 3’ end relative to the gene). Of the total number of tDMRs detected, ~25% overlapped with a CGI shore and a similar percentage with a CGI (Additional file 10: Table S3 and Additional file 5: Table S2). The number of tDMRs overlapping with CGI shelves was lower (~6%).
tDMRs are enriched in alternative transcription start sites
Functional annotation of tDMRs
tDMRs are enriched for regulatory regions
Regulatory DNA is marked by DNase I hypersensitive sites (DHSs) . DHSs were enriched for tDMRs (ORP = 1.36, ORI = 1.37, P < 10-5; Additional file 5: Table S2 and Additional file 14: Figure S9). Using ENCODE data on transcription factor binding sites (TFBSs)  we observed enrichment for tissue-specific methylation at the binding sites BCL11A (ORP = 3.22, ORI = 2.52, P < 10-5), SUZ12 (ORP = 1.71, ORI = 2.17, P < 10-5) and FOXA2 (ORP = 1.12, P = 0.30; ORI = 1.61, P < 10-5). Hypomethylation at TFBSs was observed in tissues in which the transcription factor is expressed (Additional file 15: Figure S10). For example, FOXA2 is active in the liver , pancreas  and potentially hair follicles , and FOXA2 binding sites were relatively hypomethylated in these tissues. tDMRs, however, were depleted for many other TFBSs, including for methylation-sensitive transcription factors YY1 (ORP = 0.23, ORI = 0.25, P < 10-5), Egr-1 (ORP = 0.41, ORI = 0.41, P < 10-5) and NFkB (ORP = 0.44, ORI = 0.41, P < 10-5).
Correlation of inter-individual variation across tissues
In this study we report on genome-wide methylation patterns generated using multiple peripheral and internal tissues from two independent sets of donors using 450k methylation chips. Although the 450k platform interrogates a small subset of the ~28M CpG sites in the human genome, it relatively comprehensively evaluates promoter regions and CpG islands, and also covers other potentially relevant features, including downstream genic and intergenic regions. A new algorithm was able to identify statistically robust tDMRs as illustrated by a statistically significant overlap in the location of tDMRs between the datasets. The biological relevance of the identified tDMRs was highlighted by the observation that they mapped to genes with tissue-specific expression and also showed hypomethylation specifically in the tissue expressing those genes. Annotation of tDMRs showed that they can occur irrespective of their position relative to genes or local CpG density. Tissue-specific DNA methylation was most evident, however, both absolutely and relatively, in regions outside CGIs or CGI flanking regions. This confirms previous studies reporting a high prevalence of CpG-poor regions near genes with tissue-specific expression both in humans [2, 3, 7] and animals [24, 25].
One of our key findings is that the role of non-CGI tDMRs may frequently involve the regulation of alternative transcription. Tissue-specific methylation was associated with alternative transcription start sites and, despite being sparsely covered by the 450k chip, mutually exclusive exons and cassette exons. A previous study adopting a descriptive approach combined with functional validation suggested a primary role for DNA methylation at CGIs in alternative transcription . Although we could confirm tissue-specific methylation at CGIs with a validated effect on alternative transcription from that study, our statistical approach highlighted the role of non-CGI regions in alternative transcription start sites. Interestingly, a recent study also supported a role for DNA methylation in controlling mutually exclusive exons underlining the validity of our results . The link between DNA methylation, non-CGI sequences and alternative transcription arising from our data is in line with their hypothesized role in vertebrate evolution .
Recent studies of differential methylation between tissues emphasized the occurrence of tDMRs outside non-CGI and CGI proximal promoters. For example, studies of animal models [5, 9] and subsequently humans underscored the occurrence of tDMRs in gene-body CGIs . Although the 450k chip comprehensively assesses methylation at CGIs, only ~4% of the tDMRs detected in our study mapped to a gene-body CGI. Another feature that attracted significant attention is CGI shores, which are the 2 kb regions flanking CGIs. Irizarry et al. reported that 76% of the tDMRs identified overlapped with CGI shores . Inspired by this work, the 450k chip was designed with the specific aim of covering CGI shores. Nevertheless, the percentage of CGI-shore tDMRs in our data was limited to ~25% of the total number of tDMRs. However, our data indicated that tissue-specific methylation at CGIs and CGI shores may be more relevant at downstream genic regions, which remain poorly studied. Of note, we found that differentially methylated CGI shores were associated with genes involved in housekeeping and developmental processes analogous to differentially methylated CGIs. tDMRs overlapping with so called CGI shelves (the regions flanking CGI shores) mapped to genes associated with tissue-specific processes, as was observed for non-CGI tDMRs. Our results indicate that the occurrence of tDMRs may be less biased towards previously suggested annotations including gene-body CGIs and CGI shores, and reinforce the potential utility of reconsidering current definitions of CGI annotations [12, 28–30].
The annotation of tDMRs has thus far primarily focussed on CG content and location relative to genes. Increasing knowledge of genome biology can give a more in-depth annotation. The ENCODE project mapped DNase I hypersensitive sites (DHSs), informative markers of regulatory DNA and transcription factor binding sites (TFBSs) across 349 cell lines . Both DHSs and TFBSs were enriched for tDMRs in our study. TFBS enrichment was observed for transcription factors (TFs) with a tissue-specific function and the TFBSs for these TFs were hypomethylated at TFBSs in the tissue in which they are expressed. These results are in accordance with the hypothesis that TF binding is associated with hypomethylation of TFBSs [31, 32].
Although the largest variation in DNA methylation was observed between tissues, it is more relevant to investigate inter-individual variation from the perspective of epigenetic epidemiology, which aims at identifying epigenetic risk factors for disease. Epidemiological studies, however, often have to rely on accessible peripheral tissues as proxies for internal organs directly involved in the aetiology of the disease of interest . Our exploration of the concordance between blood and internal tissues at CpG sites with variable DNA methylation suggested the presence of good correlations for a subset of variable CpG sites, many of which were locus and tissue-specific. Variable CpGs correlating across blood and all internal tissues may be primarily mediated by the effects of SNPs on DNA methylation  and may not necessarily represent a genuine epigenetic correlation. The initial evidence that blood DNA methylation may correlate to that of internal tissues as presented here and brain regions as reported previously  warrants investigations of more individuals and more tissues, such as the GTEx project , to work towards an atlas cataloguing those variably methylated regions in internal tissues that could potentially be studied indirectly by assessing their DNA methylation in specific peripheral tissues.
In conclusion, using an effective approach to detect and annotate tDMRs in 450k methylation data, we highlight the importance of non-CGI regions in tissue-specific DNA methylation and provide further evidence for a role of differential DNA methylation in the regulation of alternative transcription. Moreover, our data suggest that peripheral tissues may to some extent be used to assess inter-individual differences in DNA methylation in internal organs that frequently remain inaccessible in epidemiological studies.
DNA isolation and Illumina 450k BeadChip
For the peripheral tissue dataset, five healthy volunteers from laboratory personnel (mean age 28 years, SD = 6.1) donated blood, saliva, hair and buccal swabs after providing informed consent. DNA was isolated from the blood using the Qiagen mini kit (Qiagen, Germany) using the manufacturer’s protocol. DNA from hair follicles was also isolated using Qiagen mini kits, with the addition of 3 μL dithiothreitol (DTT) during lysis to enhance the lysis of the hair follicles. DNA was isolated from saliva using Oragene Discover kits (OGR-250, DNA Genotek Inc). DNA from buccal swabs was isolated using a chloroform/isoamyl alcohol protocol . For the internal tissue dataset, samples were taken from six cadavers within 12 h post-mortem (mean age 65.5 years, SD = 7.2; Additional file 1: Table S1). Blood was collected from the thoracic cavity in ethylenediamine-tetraacetic acid disodium salt dihydrate (EDTA) tubes (BD, United Kingdom). Tissue samples were collected and snap frozen onto a cork template with Tissue-Tek (Tissue-Tek, Netherlands). Samples were stored at −80°C until DNA extraction. To enhance lysis, tissues were sliced into 30-μm slices using a cryostat (Leica, Germany). For microscopic inspection, one 5-μm slice was stained with haematoxylin and eosin (HE). HE tissue slides were microscopically inspected to verify tissue integrity and homogeneity and to exclude inflammatory infiltrate. DNA was extracted using a chloroform/isoamyl alcohol protocol. DNA concentrations were determined using a PicoGreen dsDNA quantitation assay (Invitrogen). Bisulphite reactions were performed using the EZ-96 DNA methylation kit (Zymo Research, Orange County, USA) with an input of 1 μg of genomic DNA. After bisulphite conversion, each sample was whole-genome amplified, enzymatically fragmented, and hybridized to the Illumina HumanMethylation450 BeadChip.
This study was conducted according to the principles expressed in the Declaration of Helsinki. All samples were anonymized and procedures were performed according to the ethical guidelines in the Code for Proper Secondary Use of Human Tissue in The Netherlands (Dutch Federation of Medical Scientific Societies).
(Pre-)processing of the Illumina 450k BeadChip data
All analyses were performed in using R statistics, version 2.15.1. SNPs on the array were used to confirm that tissue samples were from the same individual and CpGs on the X and Y chromosome were used to confirm gender. CpGs with a detection P value (a value representing the measured signal compared to negative controls) over 0.05 were removed from the data. Cluster analysis (based on Euclidian distance) did not reveal signs of batch effects. The distributions of the six different signals on the 450k array (Type I (red/green and methylated/unmethylated) and Type II (red/green)) were quantile normalized separately. Quality control plots were obtained using functions from the R package minfi and custom scripts .
where is the mean methylation of tissue i of CpG j, is the overall mean methylation of CpG j and n the number of tissues studied. The cut-off we used for the effect size was a 20% difference in DNA methylation between two tissues, which equals a ≥10% difference from the overall mean (≥10% difference equals a mean sum of squares ≥0.01 since the square of 10% = 0.12). Using both an effect size and the P value cut-off, CpG sites were classified as tDMP or non-tDMP. In the second stage of the algorithm, we used the DMP status to identify DMRs, which were defined as ≥3 DMPs with an inter-CpG distance of ≤ 1 kb while allowing ≤ 3 non-DMPs in the complete DMR. This procedure assumes that the DNA methylation level of CpGs not measured using the 450k chip, but located in a tDMR called by the algorithm, are similar to the CpGs that were measured and led to the calling of a tDMR. This assumption is based on previous studies that reported high levels of co-methylation at shorter genomic distances (<1 kb) particularly in non-repeat regions (as interrogated using the 450k chip), for example, in candidate loci , in 27k data  and in whole genome bis-seq data . The presence of co-methylation was confirmed in the current dataset (Additional file 3: Figure S2B). Different settings for the inter-CpG distance (1.5 kb and 2 kb instead of 1 kb) or mismatches (1, 2, 4 and 5 instead of 3) did not appreciably alter the number and length of detected tDMRs, indicating the stability of the algorithm. The DMR finder algorithm was implemented in R statistics and the script is available in Additional file 4. The DMR finder can be used for 450k data (using Illumina CpG identifiers) as well for other types of DNA methylation data (using genomic locations).
Annotation and enrichment tests
CpGs on the 450k chip were annotated in multiple ways. First, the genome was divided according to five gene-centric regions: the inter-genic region (>10 kb from the nearest TSS), the distal promoter (−10 kb to 1.5 kb from the nearest TSS), the proximal promoter (−1.5 kb to +500 bp from the nearest TSS), the gene body (+500 bp to 3’ end of the gene) and the downstream region (3’ end to +5 kb from 3’ end). Next, CpGs were annotated as non-CGI, CGI, CGI shore or CGI shelf. Genomic locations of CpG islands were obtained from the UCSC browser . CGI shores were defined as 2 kb flanking the CpG island up- and downstream and CGI shelves as 2 kb flanking the CGI shore. Genes displaying tissue-specific expression were obtained from the TiGER database . Alternative transcription/splicing events were downloaded from Ensembl [42–44]. The DNase hypersensitive sites and transcription factor binding sites clustered for multiple cell lines as part of the ENCODE project  were downloaded from the UCSC browser. All annotations used in this paper are available from Additional file 8, Additional file 16, Additional file 17 and Additional file 18 as RData objects; these include annotations of genomic features, alternative events, DHSs and transcription factor binding sites. All annotations are based on human genome build 19.
Enrichments, that is, the gene and CpG density centric enrichments, tissue-specific expressed genes, the alternative events, the transcription factor binding sites and the DHSs were calculated using the individual CpG sites within tDMRs. All odds ratios were corrected for background enrichment, which is required because not all CpG sites on the array can become a tDMR as a result of the varying density of the chips. The background odds ratio was determined by identifying tDMR-like regions, that is, regions with an inter-CpG distance smaller than 1 kb with an average length of 5 CpGs per tDMR-like regions (cf. the number of CpGs in identified tDMRs) resulting in ~8 × 104 tDMR-like regions. Reported odds ratios are the calculated odds ratio divided by the background odds ratio. For each enrichment test, we performed 200,001 permutations with 4,500 tDMR-like regions each. Using the resulting empirical distribution, we determined the two-sided P value for enrichment.
Gene ontology term analysis
tDMRs overlapping with an annotation were mapped to the nearest gene using GREAT . Extracted genes were tested for enrichment of GO terms using the GO_BP_FAT table from the DAVID tool [46, 47]. To gain further insights regarding the major classes within the significant GO terms, the REVIGO tool was used to cluster and prune GO terms on the basis of P values obtained from DAVID, with a medium allowed similarity . Gene region figures were generated using the R package Gviz and graphs with the R package ggplot2.
To determine individual variation we used liver, subcutaneous fat, omentum and muscle from six autopsy subjects from which we obtained all these tissues. CpGs were mapped to the nearest flanking SNP using the Phase I/II CEU SNPs from the 1000 Genomes project. All SNPs in the probe and CpG SNPs were removed from the data (n = 147,963). To determine inter-individual variation we calculated the mean sum of squares for all CpG sites and selected the CpGs with a mean sum of squares >0.025. Correlations between blood and internal tissues were calculated by determining the correlation between all inter-individual comparisons in blood, compared to all inter-individual comparisons in one internal tissue and CpGs with a correlation over 0.8 were selected.
The data used in this publication have been deposited in NCBI’s Gene Expression Omnibus  and are accessible through GEO Series accession number GSE48472.
DNase I hypersensitive sites
Differentially methylated position
Differentially methylated region
Ethylenediamine-tetraacetic acid disodium salt dihydrate
- HE stain:
Hematoxylin and eosin stain
Single nucleotide polymorphism
Tissue-specific differentially methylated position
Tissue-specific differentially methylated region
Transcription factor binding site
Transcription start site.
We wish to thank Wesley de Dijcker, Maurits Drijfhout and Dennis Kremer for their excellent technical assistance; Richard Guijt and Tamara Guijt for their assistance with collecting tissues and Erik van Zwet for statistical advice. This study was financially supported by grants from the European Union’s Seventh Framework Program IDEAL (FP7/2007-2011) under grant agreement No. 259679, The National Institutes of Health (Grant AG042190-01) and the Netherlands Consortium for Healthy Ageing (Grant 05060810) within the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research.
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