ArticleProceedings of the National Academy of Sciences of the United States of America2014
Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- Methylcytosine oxidation derivatives are preferentially associated with repetitive chromatin and mark active rDNA inFrontiers in plant science · 2026Article
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- Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia.Journal of experimental botany · 2024Article
- The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development ofJournal of fungi (Basel, Switzerland) · 2023Article
- Navigating the pitfalls of mapping DNA and RNA modifications.Nature reviews. Genetics · 2023Review
- Distribution and regulatory roles of oxidized 5-methylcytosines in DNA and RNA of the basidiomycete fungiOpen biology · 2022Article
- TET-dioxygenase deficiency in oncogenesis and its targeting for tumor-selective therapeutics.Seminars in hematology · 2021Review
- TET methylcytosine oxidases: new insights from a decade of research.Journal of biosciences · 2020Review
- Microfluidic epigenomic mapping technologies for precision medicine.Lab on a chip · 2019Review
- Regulation of transposable elements by DNA modifications.Nature reviews. Genetics · 2019Review
- Article
- Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase.Nature biotechnology · 2018Article
- Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- Biochemical characterization of a Naegleria TET-like oxygenase and its application in single molecule sequencing of 5-methylcytosine.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea.PloS one · 2015Article
Corrections and comments
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Authors and funding
17 authors at 10 institutions in 1 country.
Funding
Abstract
TET/JBP enzymes oxidize 5-methylpyrimidines in DNA. In mammals, the oxidized methylcytosines (oxi-mCs) function as epigenetic marks and likely intermediates in DNA demethylation. Here we present a method based on diglucosylation of 5-hydroxymethylcytosine (5hmC) to simultaneously map 5hmC, 5-formylcytosine, and 5-carboxylcytosine at near-base-pair resolution. We have used the method to map the distribution of oxi-mC across the genome of Coprinopsis cinerea, a basidiomycete that encodes 47 TET/JBP paralogs in a previously unidentified class of DNA transposons. Like 5-methylcytosine residues from which they are derived, oxi-mC modifications are enriched at centromeres, TET/JBP transposons, and multicopy paralogous genes that are not expressed, but rarely mark genes whose expression changes between two developmental stages. Our study provides evidence for the emergence of an epigenetic regulatory system through recruitment of selfish elements in a eukaryotic lineage, and describes a method to map all three different species of oxi-mCs simultaneously.
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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.