ArticleProceedings of the National Academy of Sciences of the United States of America2004
Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed, 219 citations in OpenAlex.
- Analog epigenetic memory revealed by targeted chromatin editing.Cell genomics · 2025Article
- Homeostasis of DNA Hemi-Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strands.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Mechanistic model for epigenetic maintenance by methyl-CpG-binding domain proteins.bioRxiv : the preprint server for biology · 2024Article
- Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity.Nature structural & molecular biology · 2024Article
- Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine.Genome research · 2024Article
- Aging clocks based on accumulating stochastic variation.Nature aging · 2024Article
- Childhood environment influences epigenetic age and methylation concordance of a CpG clock locus in British-Bangladeshi migrants.Epigenetics · 2023Article
- Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species.Nature communications · 2023Article
- Exploring the crop epigenome: a comparison of DNA methylation profiling techniques.Frontiers in plant science · 2023Review
- Methylation is maintained specifically at imprinting control regions but not other DMRs associated with imprinted genes in mice bearing a mutation in theFrontiers in cell and developmental biology · 2023Article
- Review
- Identification of influential probe types in epigenetic predictions of human traits: implications for microarray design.Clinical epigenetics · 2022Article
- Evolved DNA Duplex Readers for Strand-Asymmetrically Modified 5-Hydroxymethylcytosine/5-Methylcytosine CpG Dyads.Journal of the American Chemical Society · 2022Article
- 5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer.Frontiers in molecular biosciences · 2022Review
- Hairpin-bisulfite sequencing of cells exposed to decitabine documents the process of DNA demethylation.Epigenetics · 2021Article
- The Opportunities and Challenges of Molecular Tagging Next-Generation Sequencing in Liquid Biopsy.Molecular diagnosis & therapy · 2021Article
- Origins of human disease: the chrono-epigenetic perspective.Nature reviews. Genetics · 2021Review
- From DNA damage to mutations: All roads lead to aging.Ageing research reviews · 2021Review
- DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift.Communications biology · 2021Article
40 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Epigenetic inheritance, the transmission of gene expression states from parent to daughter cells, often involves methylation of DNA. In eukaryotes, cytosine methylation is a frequent component of epigenetic mechanisms. Failure to transmit faithfully a methylated or an unmethylated state of cytosine can lead to altered phenotypes in plants and animals. A central unresolved question in epigenetics concerns the mechanisms by which a locus maintains, or changes, its state of cytosine methylation. We developed "hairpin-bisulfite PCR" to analyze these mechanisms. This method reveals the extent of methylation symmetry between the complementary strands of individual DNA molecules. Using hairpin-bisulfite PCR, we determined the fidelity of methylation transmission in the CpG island of the FMR1 gene in human lymphocytes. For the hypermethylated CpG island of this gene, characteristic of inactive-X alleles, we estimate a maintenance methylation efficiency of approximately 0.96 per site per cell division. For de novo methylation efficiency (E(d)), remarkably different estimates were obtained for the hypermethylated CpG island (E(d) = 0.17), compared with the hypomethylated island on the active-X chromosome (E(d) < 0.01). These results clarify the mechanisms by which the alternative hypomethylated and hypermethylated states of CpG islands are stably maintained through many cell divisions. We also analyzed a region of human L1 transposable elements. These L1 data provide accurate methylation patterns for the complementary strand of each repeat sequence analyzed. Hairpin-bisulfite PCR will be a powerful tool in studying other processes for which genetic or epigenetic information differs on the two complementary strands of DNA.
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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.