ArticleNature chemical biology2023
Direct enzymatic sequencing of 5-methylcytosine at single-base resolution.
Article in Nature chemical biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 47 citations in OpenAlex.
- 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
- Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies.Scientific reports · 2026Article
- Enriched methylomes of low-input and fragmented DNA using fragment ligation EXclusive methylation sequencing.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
- 5mC and 5hmC methylation sequencing: the power of 6-base sequencing in a multiomic era.Epigenomics · 2026Review
- Advancements in DNA methylation technologies and their application in cancer diagnosis.Epigenetics · 2025Review
- Targeted long-read methylation analysis using hybridization capture suitable for clinical specimens.Cell reports methods · 2025Article
- The circulating cell-free DNA landscape in sepsis is dominated by impaired liver clearance.Cell genomics · 2025Article
- A ternary-code DNA methylome atlas of mouse tissues.Genome biology · 2025Article
- Direct Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution Unravels Their Distinct Roles in Alzheimer's Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Base-resolution profiling of 5-glyceryl-methylcytosine in Chlamydomonas reinhardtii via deaminase-assisted sequencing.Nucleic acids research · 2025Article
- A DNA alteration and methylation co-detection method for clinical purpose.EMBO molecular medicine · 2025Article
- Methyl-CODEC enables simultaneous methylation and duplex sequencing.Nucleic acids research · 2025Article
- Direct single-nucleotide resolution sequencing of DNA 5-methylcytosine using engineered DNA methyltransferase-mediated CMD-seq.Chemical science · 2025Article
- Epigenetics factors in schizophrenia: future directions for etiologic and therapeutic study approaches.Annals of general psychiatry · 2025Review
- ALKBH1 knockdown promotes the growth, migration and invasion of HTR-8/SVneo cells through regulating the m5C modification PSMD14.Scientific reports · 2025Article
- Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges.MedComm · 2024Review
- Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine.Genome research · 2024Article
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16 authors at 2 institutions in 1 country.
Funding
Abstract
5-methylcytosine (5mC) is the most important DNA modification in mammalian genomes. The ideal method for 5mC localization would be both nondestructive of DNA and direct, without requiring inference based on detection of unmodified cytosines. Here we present direct methylation sequencing (DM-Seq), a bisulfite-free method for profiling 5mC at single-base resolution using nanogram quantities of DNA. DM-Seq employs two key DNA-modifying enzymes: a neomorphic DNA methyltransferase and a DNA deaminase capable of precise discrimination between cytosine modification states. Coupling these activities with deaminase-resistant adapters enables accurate detection of only 5mC via a C-to-T transition in sequencing. By comparison, we uncover a PCR-related underdetection bias with the hybrid enzymatic-chemical TET-assisted pyridine borane sequencing approach. Importantly, we show that DM-Seq, unlike bisulfite sequencing, unmasks prognostically important CpGs in a clinical tumor sample by not confounding 5mC with 5-hydroxymethylcytosine. DM-Seq thus offers an all-enzymatic, nondestructive, faithful and direct method for the reading of 5mC alone.
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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.