Reduced Bisulfite Sequencing/5-Carboxylcytosine Methylase-Assisted Bisulfite Sequencing redBS-Seq relies on the chemical reduction of 5fC to 5hmC by NaBH4. The 5hmC is detected in the same manner as 5mC (Booth et al., 2014). In caMAB-seq, 5fC is first reduced by NaBH4 to 5hmC. Owing to the […]

Post-bisulfite Adapter Tagging In PBAT, bisulfite treatment precedes adaptor tagging to avoid the bisulfite-induced fragmentation of adaptor-tagged template DNAs (Miura et al., 2012). Bisulfite treatment is followed by adapter tagging and 2 rounds of random-primer extension. This procedure generates a substantial number of unamplified reads […]

Oxidative Bisulfite Sequencing oxBS-Seq differentiates between 5mC and 5hmC (Booth et al., 2012). In this method, 5hmC is oxidized to 5fC with a selective chemical agent, while 5mC remains unchanged. Sodium bisulfite treatment of 5fC results in its deamination to uracil which, upon sequencing, is […]

Methylation-Sensitive Restriction Enzyme Sequencing MSRE/MRE-seq and Methyl-seq are protocols that use methylation-sensitive restriction enzymes (MSREs) on genomic DNA to study DNA methylation (Maunakea et al., 2010) (Brunner et al., 2009). MRE-seq enriches unmethylated DNA and can cover 1.7 million CpG sites across the human genome […]

Methylated-CpG Island Recovery Assay (MIRA) MIRA uses the high affinity of a methylated-CpG-binding protein complex (MBD2B and MBD3L1) to enrich regions with methylated CpG dinucleotides (Rauch et al., 2010). This approach can be applied to both array-based DNA analysis and NGS, which are sometimes distinguished […]

Methylated DNA Immunoprecipitation/DNA Immunoprecipitation Followed by High-Throughput Sequencing MeDIP-seq is used to study 5mC modification (Weber et al., 2005). It is based on MeDIP, originally developed as an approach for immunocapturing methylated DNA followed by microarray analysis (Weber et al., 2005). A variation on this […]

Methyl-CpG Binding Domain (MBD)_Based Capture and Sequencing / Capture of Methylated DNA Using the Methyl-CpG Binding Domain MBD domain of MeCP2 / Methyl-CpG Binding Domain_Isolated Genome Sequencing MBDCap (Rauch et al., 2008) (Rauch et al., 2009) and MethylCap (Bock et al., 2010) (Brinkman et al., […]

M.SssI Methylase-Assisted Bisulfite Sequencing MAB-seq allows simultaneous and quantitative mapping of both 5fC and 5caC at single-base resolution (Wu et al., 2014). This method is complementary to caMAB-seq, a method for direct 5caC mapping.In this method, gDNA is treated with the bacterial CpG methyltransferase M.SssI, […]

J-Binding Protein 1 Sequencing JBP1-seq is a method for genome-wide profiling of 5hmC. It relies on the strong affinity of the J-binding protein 1 (JBP1) for glucosylated 5hmC. The method uses a recombinant JBP1 protein with an additional His tag and Avi tag that is […]

Hydroxymethylated DNA Immunoprecipitation and Sequencing hMeDIP-Seq is used to study 5hmC modifications (Xu et al., 2011). It is a slight variation of MeDIP-seq, which is based on the original MeDIP method described by Weber et al (Weber et al., 2005). Although this method is technically […]