ArticleNature protocols2016
Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 32 citations in OpenAlex.
- Article
- Mapping epigenetic modifications by sequencing technologies.Cell death and differentiation · 2025Review
- An Overview of Global, Local, and Base-Resolution Methods for the Detection of 5-Hydroxymethylcytosine in Genomic DNA.Methods in molecular biology (Clifton, N.J.) · 2024Review
- 5-hydroxymethylcytosines regulate gene expression as a passive DNA demethylation resisting epigenetic mark in proliferative somatic cells.bioRxiv : the preprint server for biology · 2023Article
- Factors and Methods for the Detection of Gene Expression Regulation.Biomolecules · 2023Review
- Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers.Development (Cambridge, England) · 2022Review
- Quantification and mapping of DNA modifications.RSC chemical biology · 2021Review
- Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection.Nucleic acids research · 2021Article
- Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency.Molecular cell · 2021Article
- Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution.Nature communications · 2021Article
- Mapping the epigenetic modifications of DNA and RNA.Protein & cell · 2020Review
- methyl-ATAC-seq measures DNA methylation at accessible chromatin.Genome research · 2019Article
- Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.Nature biotechnology · 2019Article
- Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells.Genes & development · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
A complete understanding of the function of the ten-eleven translocation (TET) family of dioxygenase-mediated DNA demethylation requires new methods to quantitatively map oxidized 5-methylcytosine (5mC) bases at high resolution. We have recently developed a methylase-assisted bisulfite sequencing (MAB-seq) method that allows base-resolution mapping of 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), two oxidized 5mC bases indicative of active DNA demethylation events. In standard bisulfite sequencing (BS-seq), unmodified C, 5fC and 5caC are read as thymine; thus 5fC and 5caC cannot be distinguished from C. In MAB-seq, unmodified C is enzymatically converted to 5mC, allowing direct mapping of rare modifications such as 5fC and 5caC. By combining MAB-seq with chemical reduction of 5fC to 5hmC, we also developed caMAB-seq, a method for direct 5caC mapping. Compared with subtraction-based mapping methods, MAB-seq and caMAB-seq require less sequencing effort and enable robust statistical calling of 5fC and/or 5caC. MAB-seq and caMAB-seq can be adapted to map 5fC/5caC at the whole-genome scale (WG-MAB-seq), within specific genomic regions enriched for enhancer-marking histone modifications (chromatin immunoprecipitation (ChIP)-MAB-seq), or at CpG-rich sequences (reduced-representation (RR)-MAB-seq) such as gene promoters. The full protocol, including DNA preparation, enzymatic treatment, library preparation and sequencing, can be completed within 6-8 d.
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Registered trials
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