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Table 1 Experimental approaches for profiling genome-wide DNA methylation

From: Profiling genome-wide DNA methylation

Experimental approach Strength Weakness Resolution Quantitative nature Cost Examples References
CHARM -Cost-effective
-Interrogate CpG sites genome-wide irrespective of proximity to genes or CpG islands
-Moderate resolution
-Limited to regions in proximity to enzymes’ recognition sites
Abundance Low CGI shores show alteration DNA methylation in colon cancer [36] [34]
MBDCap-Seq -Cost-effective
-Allow the detection of DMRs within highly CpG-dense regions and regions with lower CpG density
-MBD proteins can discriminate 5mC from 5hmC
-No mutation introduced
-More sensitive than MeDIP in regions with higher CpG density
-Relatively low resolution
-Biased toward hypermethylated regions
~150 bp Abundance Moderate Confirmed previous known differentially methylated sites and discovered new differentially methylated loci in 3 isogenic colon cancer cell lines [38] [37]
MeDIP -Cost-effective
-No mutation introduced
-Specific to 5mC/5hmC depending on the antibody specificity
-More sensitive in regions with low CpG density than MBDCap-Seq
-Biased toward hypermethylated regions
-Do not identify individual 5mC sites
-Inability to predict absolute methylation level
~100 bp Abundance Moderate MBDCap-seq shows higher genomic coverage than MeDIP-seq along with twice as many DMRs between colon cancer and adjacent normal cells [45] [39, 42]
Illumina’s Infinium Methylation assay -Cost-effective
-Do not require a large amount of input DNA
-Human sample only
-Coverage is highly dependent on the array design
-Substantial DNA degradation after bisulfite treatment
Single base Abundance Low DNA methylation as a signature to surrogate different cord blood cell types [49] [47]
WGBS Evaluate methylation state of almost every CpG sites -High cost
-Substantial DNA degradation after bisulfite treatment
-Cannot discriminate between 5mC and 5hmC
Single base Digital High Bulk methylation level of CpG/CHG/CHH of wild-type Arabidopsis and methyltransferase-deficient mutants [18]
Genome-wide methylation pattern and site-specific methylation [18]
Global demethylation in the endosperm compared to the embryo [55]
[52]
RRBS -High CGI coverage
-High sensitivity
-Cost-effective comparing to WGBS
-May exhibit a lack of coverage at intergenic and distal regulatory elements
-Substantial DNA degradation after bisulfite treatment
-Limited to regions in proximity to enzymes’ recognition sites
-Cannot discriminate between 5mC and 5hmC
Single base Digital Moderate The EWAS study integrating DNA methylation, gene expression, proteomics, metabolomics and clinical traits in 90 mouse inbred strains [62] [60, 61]
scWGBS Able to study methylome intra-population distribution -Low sequencing efficiency (~20 million reads typically required per cell)
-Cannot discriminate between 5mC and 5hmC
Single base Digital High Determining epigenomic cell-state dynamics in mouse pluripotent and differentiating cells [74] [72, 74]
scRRBS -Highly sensitive
-Can detect target CpG sites at high coverage with relatively low number of sequence reads
-Substantial DNA degradation after bisulfite treatment
-Cannot discriminate between 5mC and 5hmC
-Provide relatively poor coverage for imprinting loci
Single base Digital High Profiling epigenomic dynamics of 1 million CpG sites during early embryonic development in ESCs [70] [70]
TAB-seq Can distinguish 5hmC from 5mC -Substantial DNA degradation after bisulfite treatment
-Tet enzyme with low efficiency might leave methylated residues unconverted
-High sequencing depth is required to detect 5hmC with low abundance
Single base Digital High Profiling 5hmC distribution in 108 days human PGCs to reveal DNA demethylation [83] [81]