ArticleFrontiers in genetics2014
Methylated DNA is over-represented in whole-genome bisulfite sequencing data.
Article in Frontiers in genetics, 2014. 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.
- A translocation within the Ogataea species complex alters local subtelomeric chromatin while maintaining overall genome organization.G3 (Bethesda, Md.) · 2026Article
- Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation.Nature communications · 2026Article
- FINE-EM-seq: a rapid isothermal amplification method enabling comprehensive methylome profiling of zebrafish early embryos.Cell insight · 2026Article
- A Translocation within thebioRxiv : the preprint server for biology · 2026Article
- Centromeres are hotspots of cytosine methylation epimutations in a filamentous fungus.bioRxiv : the preprint server for biology · 2026Article
- The Double-Edged Sword of Genomic DNA Methylation: Orchestrating Gastric Carcinogenesis and Shaping Precision Oncology.Oncology research · 2026Review
- Article
- Leveraging sequences missing from the human genome to diagnose cancer.Communications medicine · 2025Article
- Assessing DNA methylation detection for primary human tissue using Nanopore sequencing.Genome research · 2025Article
- Integrative analysis of the methylome and transcriptome of tomato fruit (Horticulture research · 2024Article
- A signal processing and deep learning framework for methylation detection using Oxford Nanopore sequencing.Nature communications · 2024Article
- Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing.Genome medicine · 2023Article
- The genome organization of Neurospora crassa at high resolution uncovers principles of fungal chromosome topology.G3 (Bethesda, Md.) · 2022Article
- scTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs.Scientific reports · 2022Article
- RNA Pol IV induces antagonistic parent-of-origin effects on Arabidopsis endosperm.PLoS biology · 2022Article
- Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies.Small methods · 2022Review
- Article
- Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.Advances in experimental medicine and biology · 2022Article
- Nanopore Sequencing and Data Analysis for Base-Resolution Genome-Wide 5-Methylcytosine Profiling.Methods in molecular biology (Clifton, N.J.) · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The development of whole-genome bisulfite sequencing (WGBS) has resulted in a number of exciting discoveries about the role of DNA methylation leading to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently advanced to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of reads from methylated DNA in WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. It is especially critical for studies that seek to accurately quantify DNA methylation levels in populations that may segregate for allelic DNA methylation states.
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