ArticleBMC genomics2013
Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Multiplexed single-cell reduced representation bisulfite sequencing for genome-wide DNA methylation profiling.Nature protocols · 2026Review
- RSPO4 exerts tumor suppression through antagonizing canonical and non-canonical Wnt signaling.International journal of biological sciences · 2026Article
- Examination of DNA Methylation Patterns in Children Born Premature with Prenatal Tobacco Smoke Exposure.Toxics · 2025Article
- The Gut Microbiome and Epigenomic Reprogramming: Mechanisms, Interactions, and Implications for Human Health and Disease.International journal of molecular sciences · 2025Review
- Analysis of DNA methylation changes following Cfp1 knockout in mouse spermatocytes.Animal bioscience · 2025Article
- Unlocking the Potential of Liquid Biopsy: A Paradigm Shift in Endometrial Cancer Care.Diagnostics (Basel, Switzerland) · 2025Review
- Genome-wide DNA methylation and transcriptome sequencing analyses of lens tissue in an age-related mouse cataract model.PloS one · 2025Article
- Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA.Nucleic acids research · 2024Article
- Forkhead box E1, frequently downregulted by promoter methylation, inhibits colorectal cancer cell growth and migration.Cancer cell international · 2024Article
- Shortcut barcoding and early pooling for scalable multiplex single-cell reduced-representation CpG methylation sequencing at single nucleotide resolution.Nucleic acids research · 2023Article
- Advances in DNA methylation and demethylation in medicinal plants: a review.Molecular biology reports · 2023Review
- Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species.Nature communications · 2023Article
- Technologies and applications of single-cell DNA methylation sequencing.Theranostics · 2023Review
- Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation.Nature genetics · 2022Article
- Next generation sequencing technologies to explore the diversity of germplasm resources: Achievements and trends in tomato.Computational and structural biotechnology journal · 2022Review
- Smart-RRBS for single-cell methylome and transcriptome analysis.Nature protocols · 2021Review
- Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.).BMC genomics · 2021Article
- Cell-Free DNA-Methylation-Based Methods and Applications in Oncology.Biomolecules · 2020Review
- The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth.The plant genome · 2020Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundReduced representation bisulfite sequencing (RRBS) was developed to measure DNA methylation of high-CG regions at single base-pair resolution, and has been widely used because of its minimal DNA requirements and cost efficacy; however, the CpG coverage of genomic regions is restricted and important regions with low-CG will be ignored in DNA methylation profiling. This method could be improved to generate a more comprehensive representation.
resultsBased on in silico simulation of enzyme digestion of human and mouse genomes, we have optimized the current single-enzyme RRBS by applying double enzyme digestion in the library construction to interrogate more representative regions. CpG coverage of genomic regions was considerably increased in both high-CG and low-CG regions using the double-enzyme RRBS method, leading to more accurate detection of their average methylation levels and identification of differential methylation regions between samples. We also applied this double-enzyme RRBS method to comprehensively analyze the CpG methylation profiles of two colorectal cancer cell lines.
conclusionThe double-enzyme RRBS increases the CpG coverage of genomic regions considerably over the previous single-enzyme RRBS method, leading to more accurate detection of their average methylation levels. It will facilitate genome-wide DNA methylation studies in multiple and complex clinical samples.
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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.