ArticleGenome research2018
Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
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Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Associations of maternal night shift work during pregnancy with DNA methylation in offspring: a meta-analysis in the PACE consortium.Clinical epigenetics · 2025Pooled it
- XIST drives X-chromosome inactivation and safeguards female extraembryonic cells in humans.Nature communications · 2026Article
- Predictive Value of Perfusate Cell-free DNA During Hypothermic and Normothermic Machine Perfusion of Donor Kidneys.Transplantation direct · 2026Article
- Prognostic value of peri-operative circulating tumour DNA levels estimated by cell-free DNA methylation in patients with resectable colorectal liver metastases.EBioMedicine · 2026Article
- Improved circulating tumor DNA profiling by simultaneous extraction of DNA methylation and copy number information from methylated DNA sequencing data.NPJ precision oncology · 2025Article
- Methylated CfDNA may distinguish between high- and intermediate-risk uveal melanoma: a pilot study.Cancer cell international · 2025Article
- Genome-wide methylation profiles of primary and matched distant metastasis: insights from the Dutch Early-Stage melanoma (D-ESMEL) study.Human genomics · 2025Article
- Advancements in DNA methylation technologies and their application in cancer diagnosis.Epigenetics · 2025Review
- The technology landscape for detection of DNA methylation in cancer liquid biopsies.Epigenetics · 2025Review
- A comparative study of four cell-free DNA assays for detecting circulating tumor DNA in early breast cancer.Breast cancer research : BCR · 2025Article
- Genome-Wide Methylation Sequencing to Identify DNA Methylation Markers for Early-stage Hepatocellular Carcinoma in Liver and Blood.Journal of experimental & clinical cancer research : CR · 2025Article
- Profiling (placental) DNA methylation in cell-free DNA across gestation: the Rotterdam Periconception Cohort.Molecular human reproduction · 2025Article
- Investigating Single-Molecule Molecular Inversion Probes for Medium-Scale Targeted DNA Methylation Analysis.Epigenomes · 2025Article
- Genome-wide methylation profiling of maternal cell-free DNA using methylated DNA sequencing (MeD-seq) indicates a placental and immune-cell signature.European journal of clinical investigation · 2025Article
- Integrating advanced analytical methods to assess epigenetic marks affecting response to hypomethylating agents in higher risk myelodysplastic syndrome.Molecular medicine (Cambridge, Mass.) · 2025Article
- Article
- Evaluation for CpG island methylation of FASN and SREBP promoter in Mongolian gerbil NAFLD model.Archives of medical science : AMS · 2025Article
- Clinical promise and applications of epigenetic biomarkers.Clinical epigenetics · 2024Article
- Genome-wide methylation analysis in patients with proximal hypospadias - a pilot study and review of the literature.Epigenetics · 2024Review
- XIST dampens X chromosome activity in a SPEN-dependent manner during early human development.Nature structural & molecular biology · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is a well-known epigenetic modification that plays a crucial role in gene regulation, but genome-wide analysis of DNA methylation remains technically challenging and costly. DNA methylation-dependent restriction enzymes can be used to restrict CpG methylation analysis to methylated regions of the genome only, which significantly reduces the required sequencing depth and simplifies subsequent bioinformatics analysis. Unfortunately, this approach has been hampered by complete digestion of DNA in CpG methylation-dense regions, resulting in fragments that are too small for accurate mapping. Here, we show that the activity of DNA methylation-dependent enzyme, LpnPI, is blocked by a fragment size smaller than 32 bp. This unique property prevents complete digestion of methylation-dense DNA and allows accurate genome-wide analysis of CpG methylation at single-nucleotide resolution. Methylated DNA sequencing (MeD-seq) of LpnPI digested fragments revealed highly reproducible genome-wide CpG methylation profiles for >50% of all potentially methylated CpGs, at a sequencing depth less than one-tenth required for whole-genome bisulfite sequencing (WGBS). MeD-seq identified a high number of patient and tissue-specific differential methylated regions (DMRs) and revealed that patient-specific DMRs observed in both blood and buccal samples predict DNA methylation in other tissues and organs. We also observed highly variable DNA methylation at gene promoters on the inactive X Chromosome, indicating tissue-specific and interpatient-specific escape of X Chromosome inactivation. These findings highlight the potential of MeD-seq for high-throughput epigenetic profiling.
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