ArticleMethods (San Diego, Calif.)2007
Single-molecule and population probing of chromatin structure using DNA methyltransferases.
Article in Methods (San Diego, Calif.), 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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.
The trial behind it
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
27 citing papers in PubMed, 44 citations in OpenAlex.
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Article
- FENGC: Targeted, Multiplexed, and Integrated Single-Molecule Profiling of Chromatin Accessibility and DNA Methylation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A single fiber view of the nucleosome organization in eukaryotic chromatin.Nucleic acids research · 2024Article
- Mapping nucleosome and chromatin architectures: A survey of computational methods.Computational and structural biotechnology journal · 2022Review
- Cytosine-5 methylation-directed construction of a Au nanoparticle-based nanosensor for simultaneous detection of multiple DNA methyltransferases at the single-molecule level.Chemical science · 2020Article
- Beads on a string-nucleosome array arrangements and folding of the chromatin fiber.Nature structural & molecular biology · 2020Review
- Absolute nucleosome occupancy map for theGenome research · 2019Article
- Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data.Nucleic acids research · 2019Article
- Epigenetic landscape change analysis during human EMT sheds light on a key EMT mediator TRIM29.Oncotarget · 2017Article
- Article
- Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer.Genome research · 2014Article
- Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma.Genome research · 2014Article
- The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin.Nucleic acids research · 2014Review
- Local depletion of DNA methylation identifies a repressive p53 regulatory region in the NEK2 promoter.The Journal of biological chemistry · 2013Article
- DNA methylation and nucleosome occupancy regulate the cancer germline antigen gene MAGEA11.Epigenetics · 2013Article
- Identification of DNMT1 selective antagonists using a novel scintillation proximity assay.The Journal of biological chemistry · 2013Article
- Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus.Nucleic acids research · 2013Article
- Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.Genome research · 2012Article
- DNA methyltransferase accessibility protocol for individual templates by deep sequencing.Methods in enzymology · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Probing chromatin structure with DNA methyltransferases offers advantages over more commonly used nuclease-based and chromatin immunoprecipitation methods for detection of nucleosomes and non-histone protein-DNA interactions. Here, we describe two related methods in which the readout of MTase accessibility is obtained by assaying 5-methylcytosine in DNA through the PCR-based technique of bisulfite genomic sequencing. The methyltransferase accessibility protocol (MAP) determines the relative frequency at which the enzyme accesses each of its target sites over an entire population of PCR amplified product. While MAP yields much quantitative information about relative accessibility of a region of chromatin, a complementary single-molecule view of methyltransferase accessibility, termed MAP for individual templates (MAP-IT), is provided by analysis of cloned PCR products. Absolute rather than relative methylation frequencies in a region are obtained by summing the methylation status at each site over a cohort of clones. Moreover, as the integrity of individual molecules is maintained in MAP-IT, unique information about the distribution of multiple footprints along continuous regions is gleaned. In principle, the population MAP and single-molecule MAP-IT strategies can be used to analyze chromatin structure in a variety of model systems. Here, we describe the application of MAP in living Saccharomyces cerevisiae cells and MAP-IT in the analysis of a mammalian tumor suppressor gene in nuclei. This application of MAP-IT provides the first means to simultaneously determine CpG methylation of mammalian genes and their overlying chromatin structure in the same single DNA molecule.
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What OpenQuestion holds
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.