A 5-Formylcytosine-Selective Chemical Labeling In demethylation pathways, the TET family of proteins oxidize 5mC to 5hmC, 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in a stepwise fashion. Conversely, in vivo, 5fmC residues can be converted to cytosine by base-excision repair.In fC-Seal, 5hmC residues in the genome are […]

5fC Chemical Labeling and C-to-T Transition During PCR fC-CET is a bisulfite-free method for whole-genome analysis of 5fC. The method is based on selective chemical labeling of 5fC and subsequent C-to-T transition during PCR (Xia et al., 2015). In this method, gDNA is labeled sequentially […]

5-Formylcytosine Chemical Modification_Assisted Bisulfite Sequencing fCAB-Seq is a method for EtONH2-modified bisulfite sequencing for base-resolution detection of 5fC in gDNA (Song et al., 2013). It is complementary to fC-Seal, which was developed as a highly selective chemical labeling approach for the affinity purification and genome-wide […]

Double-Digest Restriction Site_Associated DNA Marker Generation with a Methylation-Sensitive Restriction Enzyme EpiRADseq is similar to the widely used double-digest RAD-seq method (ddRADseq), except that it uses an MSRE Schield et al., 2016). DNA samples are digested with PstI and HpaII followed by purification. Double-stranded sequencing […]

Chemical Modification_Assisted Bisulfite Sequencing CAB-Seq can detect 5caC with single-base resolution in DNA (Lu et al., 2013). It is based on the observation that chemically modified 5caC can survive bisulfite treatment without deamination.Advantages: Single-base resolutionDisadvantages: Relatively low protection rate of 5caC deamination (50_60%) (Wu et […]

Whole-Genome Bisulfite Sequencing BS-Seq/Bisulfite-seq or WGBS is a well-established protocol to detect methylated cytosines in gDNA (Feil et al., 1994). In this method, gDNA is treated with sodium bisulfite and then sequenced, providing single-base resolution of methylated cytosines in the genome. Upon bisulfite treatment, unmethylated […]

Bisulfite Sequencing With Padlock Probes BSPP is a targeted method that isolates selected locations for methylation profiling (Deng et al., 2009) (Ball et al., 2009). Padlock probes are ~100 nt DNA fragments designed to hybridize to genomic DNA targets in a horseshoe manner. After the […]

Bisulfite Amplicon Sequencing BSAS is a targeted BS-Seq method that uses PCR enrichment of targeted regions and transposome-mediated library construction for rapid generation of sequencing libraries, from low (1 ng) sample input (Masser et al., 2013).Genomic DNA is bisulfite-converted and subjected to PCR, using primers […]

Bisulfite-Treated Chromatin-Immunoprecipitated DNA / ChIP of Bisulfite-treated chromatin-Bisulfite Sequencing / Chromatin Immunoprecipitation with Bisulfite Methylation Sequencing Assay BisChIP-seq, ChIP-BS-seq, and ChIP-BMS all refer to essentially the same method (Plongthongkum et al., 2014). It is a direct, quantitative approach to assess DNA methylation patterns associated with […]

AbaSI Coupled with Sequencing Aba-seq is a method for high-resolution mapping of the 5hmC methylome that provides sensitive detection of 5hmC at low-occupancy regions (Sun et al., 2013). The method relies on the unique property of the restriction enzyme AbaSI to recognize glucosylated 5hmC with […]