ArticleNature biotechnology2018
Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase.
Article in Nature biotechnology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
113 citing papers in PubMed, 230 citations in OpenAlex.
- Epigenetic regulation of humoral immunity: molecular mechanisms, diseases and therapeutic targets.Signal transduction and targeted therapy · 2026Review
- Genomic sequence context differentially impacts stepwise oxidation by TET enzymes to shape DNA hydroxymethylation landscapes.Nucleic acids research · 2026Article
- A theoretical and experimental framework enables low-coverage sequencing for accurate quantification of genome-wide cytosine modification levels.NAR genomics and bioinformatics · 2026Article
- Simultaneous single-base resolution profiling of 5mC and 5hmC using BRIGHT-seq.National science review · 2026Article
- Mapping Protein Occupancy on DNA with an Unnatural Cytosine Modification.ACS chemical biology · 2026Article
- Establishment and Performance Evaluation of a Multiplexed TET2-APOBEC-Mediated cfDNA Methylation Detection Workflow Using qPCR and dPCR Readouts.Journal of personalized medicine · 2026Article
- Chemiluminescent Deoxyribozyme Sensors for DNA-Editing Enzymes.ACS chemical biology · 2026Article
- HM-DyadCap - capture and mapping of 5-hydroxymethylcytosine/5-methylcytosine CpG dyads in mammalian DNA.Nucleic acids research · 2026Article
- Unnatural Cytosine Analogs Potentiate a Customizable, Enzymatic Method for Integrated Epigenetic and Four-Base Genetic Sequencing.Journal of the American Chemical Society · 2026Article
- Mammalian Proteome Profiling Reveals Readers and Antireaders of Strand-Symmetric and -Asymmetric 5-Hydroxymethylcytosine-Modifications in DNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Deaminase-Assisted Sequencing for the Identification of 5-glyceryl-methylcytosine.Bio-protocol · 2026Article
- Sequencing DNA methylation and hydroxymethylation at co-occurring chromatin features.Nature communications · 2026Article
- The role of cytosine modification symmetry in mammalian epigenome regulation.Chemical science · 2026Review
- Selective rolling circle amplification detection of site-specific DNA 5-hydroxymethylcytosine.Frontiers in immunology · 2026Article
- TET-mediated 5hmC in breast cancer: mechanism and clinical potential.Epigenetics · 2025Review
- Effective in vivo RNA base editing via engineered cytidine deaminase APOBECs fused with PUF proteins.Nature communications · 2025Article
- An unnatural base pair for the detection of epigenetic cytosine modifications in DNA.Nature chemistry · 2025Article
- KnowYourCG: Facilitating base-level sparse methylome interpretation.Science advances · 2025Article
- A ternary-code DNA methylome atlas of mouse tissues.Genome biology · 2025Article
- Comprehensive comparison of enzymatic and bisulfite DNA methylation analysis in clinically relevant samples.Clinical epigenetics · 2025Article
53 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
Here we present APOBEC-coupled epigenetic sequencing (ACE-seq), a bisulfite-free method for localizing 5-hydroxymethylcytosine (5hmC) at single-base resolution with low DNA input. The method builds on the observation that AID/APOBEC family DNA deaminase enzymes can potently discriminate between cytosine modification states and exploits the non-destructive nature of enzymatic, rather than chemical, deamination. ACE-seq yielded high-confidence 5hmC profiles with at least 1,000-fold less DNA input than conventional methods. Applying ACE-seq to generate a base-resolution map of 5hmC in tissue-derived cortical excitatory neurons, we found that 5hmC was almost entirely confined to CG dinucleotides. The whole-genome map permitted cytosine, 5-methylcytosine (5mC) and 5hmC to be parsed and revealed genomic features that diverged from global patterns, including enhancers and imprinting control regions with high and low 5hmC/5mC ratios, respectively. Enzymatic deamination overcomes many challenges posed by bisulfite-based methods, thus expanding the scope of epigenome profiling to include scarce samples and opening new lines of inquiry regarding the role of cytosine modifications in genome biology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.