ArticleNucleic acids research2022
Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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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.
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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.
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Who cites it
23 citing papers in PubMed, 32 citations in OpenAlex.
- DNA Methylation as a Programmable Information Layer: From Molecular Marks to Disease State Engineering.International journal of molecular sciences · 2026Review
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Advances, opportunities, and challenges in microbial community construction: from environmental remediation to biomanufacturing.Archives of microbiology · 2026Review
- Optimized primer and model improve precision of X chromosome telomere length determination in the Han population.iScience · 2026Article
- Epigenetic regulation in prokaryotes: transcriptional and phenotypic outcomes of DNA methyltransferase activity.FEMS microbiology reviews · 2026Review
- DNA methylation as a biomarker of prenatal exposures: current challenges and opportunities.Environmental epigenetics · 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
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- Multi-platform framework for mapping somatic retrotransposition in human tissues.bioRxiv : the preprint server for biology · 2025Article
- Direct single-nucleotide resolution sequencing of DNA 5-methylcytosine using engineered DNA methyltransferase-mediated CMD-seq.Chemical science · 2025Article
- DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches.Journal of translational medicine · 2025Review
- Investigating Single-Molecule Molecular Inversion Probes for Medium-Scale Targeted DNA Methylation Analysis.Epigenomes · 2025Article
- From chromatin to crop: epigenetic innovations in bioenergy systems.Frontiers in plant science · 2025Review
- Mapping epigenetic modifications by sequencing technologies.Cell death and differentiation · 2025Review
- Methods for Detection and Mapping of Methylated and Hydroxymethylated Cytosine in DNA.Biomolecules · 2024Review
- Local read haplotagging enables accurate long-read small variant calling.Nature communications · 2024Article
- Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA.Nature structural & molecular biology · 2024Article
- Circulating cell-free DNA-based methylation pattern in plasma for early diagnosis of esophagus cancer.PeerJ · 2024Review
- Local read haplotagging enables accurate long-read small variant calling.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2× depth, we discovered a significant proportion of CpG sites that were not covered in previous 27.5× short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.
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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.