ArticleMethods in enzymology2016
Quantification of Oxidized 5-Methylcytosine Bases and TET Enzyme Activity.
Article in Methods in enzymology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 40 citations in OpenAlex.
- Genomic sequence context differentially impacts stepwise oxidation by TET enzymes to shape DNA hydroxymethylation landscapes.Nucleic acids research · 2026Article
- Cytosine methylase and hydroxymethylase activity in mammalian mitochondria.Frontiers in cell and developmental biology · 2025Article
- Pioneering contribution of Professor Bruce Ames to early development in biochemical aspects of oxidatively generated damage to DNA.Frontiers in molecular biosciences · 2025Review
- Development of a rapid mass spectrometric method for the analysis of ten-eleven translocation enzymes.Methods in enzymology · 2024Article
- 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
- A high-throughput effector screen identifies a novel small molecule scaffold for inhibition of ten-eleven translocation dioxygenase 2.RSC medicinal chemistry · 2022Article
- Renal oncometabolite L-2-hydroxyglutarate imposes a block in kidney tubulogenesis: Evidence for an epigenetic basis for the L-2HG-induced impairment of differentiation.Frontiers in endocrinology · 2022Article
- 5-Hydroxymethyl-, 5-Formyl- and 5-Carboxydeoxycytidines as Oxidative Lesions and Epigenetic Marks.Chemistry (Weinheim an der Bergstrasse, Germany) · 2021Article
- TET-TDG Active DNA Demethylation at CpG and Non-CpG Sites.Journal of molecular biology · 2021Article
- Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency.Molecular cell · 2021Article
- Discovery of an Unnatural DNA Modification Derived from a Natural Secondary Metabolite.Cell chemical biology · 2021Article
- TET2 chemically modifies tRNAs and regulates tRNA fragment levels.Nature structural & molecular biology · 2021Article
- Harnessing Alternative Substrates to Probe TET Family Enzymes.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Modular affinity-labeling of the cytosine demethylation base elements in DNA.Scientific reports · 2020Article
- Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N-Demethylation.Angewandte Chemie (International ed. in English) · 2020Article
- Selectivity and Promiscuity in TET-Mediated Oxidation of 5-Methylcytosine in DNA and RNA.Biochemistry · 2019Article
- Exploiting Substrate Promiscuity To Develop Activity-Based Probes for Ten-Eleven Translocation Family Enzymes.Journal of the American Chemical Society · 2018Article
- Article
- High Performance Liquid Chromatography Separation of Epigenetic Cytosine Variants.Methods and protocols · 2018Article
- A rapid mass spectrometric method for the measurement of catalytic activity of ten-eleven translocation enzymes.Analytical biochemistry · 2017Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
In eukaryotic DNA, cytosine can be enzymatically modified to yield up to four epigenetic base variants. DNA methyltransferases convert cytosine to 5-methylcytosine (mC), which plays critical roles in gene regulation during development. Ten-eleven translocation (TET) enzymes can sequentially oxidize mC to three products: 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC). These oxidized bases have been found in numerous mammalian cell types, where they potentially carry out independent epigenetic functions and aid in DNA demethylation. To gain insight into the mechanisms and functions of TET family enzymes, rigorous approaches are needed to quantify genomic cytosine modifications in cells and track TET enzyme activity in vitro. Here, we present tools developed by our lab and others to report on each of the five forms of cytosine (unmodified, mC, hmC, fC, and caC) with high specificity and sensitivity. We provide detailed protocols for qualitative and quantitative analysis of cytosine modifications in genomic DNA by dot blotting and LC-MS/MS. We then describe methods for generating synthetic oligonucleotide substrates for biochemical studies, provide optimized reaction conditions, and introduce several chemoenzymatic assays, as well as HPLC, mass spectrometry, and scintillation counting methods to quantify cytosine modifications in vitro. These approaches enable mechanistic studies of TET activity, which are key to understanding the role of these enzymes in epigenetic regulation.
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