Evidence map›Paper›PMID 41673887›Full record

ArticleGenome biology2026

DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

Yiding Wang, Yang Li, Chang Ye, Iryna Irkliyenko, Lu Gao, Marc Bissonnette, Qing Dai, Weixin Tang, Chuan He

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Yiding Wang *Committee on Genetics, Genomics & System Biology, The University of Chicago, Chicago, IL, USA.
Yang Li *Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
Chang Ye *Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
Iryna IrkliyenkoUniversity of California, Berkeley-University of California, San Francisco, USA.
Lu GaoDepartment of Chemistry, The University of Chicago, Chicago, IL, USA.
Marc BissonnetteDepartment of Medicine, The University of Chicago, Chicago, IL, USA.
Qing DaiHoward Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
Weixin TangDepartment of Chemistry, The University of Chicago, Chicago, IL, USA.
Chuan HeHoward Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. chuanhe@uchicago.edu.

Funding

Labeling and sequencing of 5hmC and 5mC in DNA-RenewalR01HG006827 · NHGRI · UNIVERSITY OF CHICAGO · PI HE, CHUAN · 2012 to 2025
$7.2M
Enriching and Base-Resolution Profiling of 5-Methylcytosine in Degraded Clinical SamplesR61CA297947 · NCI · UNIVERSITY OF CHICAGO · PI Weixin Tang · 2025 to 2026
$624k
NIH HHS R01 HG006827NIH HHS R61 CA297947
6 · The paper itself

Abstract

Various methods have been developed for 5-methylcytosine (5mC) sequencing; however, effective ways to enrich hypomethylated DNA regions have been limited. Here, we describe the DEMETER-assisted 5-Methylcytosine Nicking sequencing (DMN-seq) utilizing 5mC-specific glycosylase DEMETER to nick DNA at 5mC sites, enabling 5mC detection at the single-base resolution. Leveraging this nicking activity to deplete hypermethylated sites, we adapt DMN-seq to preferentially enrich and investigate hypomethylated regions in colorectal cancer samples. When applied to cell-free DNA as low as 0.1 ng, DMN-seq significantly expands the scope of cancer biomarkers by capturing hypomethylated regions, with high sensitivity and reproducibility even in low-input clinical samples.

Indexed as

Biomarkers, TumorDNA GlycosylasesDNA MethylationSequence Analysis, DNA5-MethylcytosineColorectal NeoplasmsHumans5-MethylcytosineBiomarkers, TumorDNA GlycosylasesBiomarker discoveryCancer detectionCell-free DNADNA 5-methylcystosine sequencingDNA hypomethylation sequencingLow-input DNA

Identifiers

PMID41673887
PMCPMC13097799

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Registered trials

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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.