ArticleNucleic acids research2015
Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed, 56 citations in OpenAlex.
- Epigenetics in development, disease, and therapy: from mechanisms to clinical interventions.Science China. Life sciences · 2026Review
- EnDeep4mC predicts DNAGenome research · 2026Article
- Replication-coupled hemimethylation inFrontiers in microbiology · 2026Review
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA.Nature biotechnology · 2024Article
- Emerging methylation-based approaches in microbiome engineering.Biotechnology for biofuels and bioproducts · 2024Review
- MLACNN: an attention mechanism-based CNN architecture for predicting genome-wide DNA methylation.Theory in biosciences = Theorie in den Biowissenschaften · 2023Article
- Shaping eukaryotic epigenetic systems by horizontal gene transfer.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Navigating the pitfalls of mapping DNA and RNA modifications.Nature reviews. Genetics · 2023Review
- Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis.Scientific reports · 2023Article
- MultiScale-CNN-4mCPred: a multi-scale CNN and adaptive embedding-based method for mouse genome DNA N4-methylcytosine prediction.BMC bioinformatics · 2023Article
- m4C DNA methylation regulates biosynthesis of daptomycin inSynthetic and systems biotechnology · 2022Article
- Genome-wide mapping ofChemical science · 2022Article
- Means, mechanisms and consequences of adenine methylation in DNA.Nature reviews. Genetics · 2022Review
- Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction.BMC bioinformatics · 2022Article
- NT-seq: a chemical-based sequencing method for genomic methylome profiling.Genome biology · 2022Article
- Systematic Analysis and Accurate Identification of DNA N4-Methylcytosine Sites by Deep Learning.Frontiers in microbiology · 2022Article
- Quantification and mapping of DNA modifications.RSC chemical biology · 2021Review
- DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites.Briefings in bioinformatics · 2021Article
- Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning.Briefings in bioinformatics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic engineering of bacterial species. Systematic identification of DNA methylation in R-M systems, including N(6)-methyladenine (6mA), 5-methylcytosine (5mC) and N(4)-methylcytosine (4mC), will enable strategies to make these species genetically tractable. Although single-molecule, real time (SMRT) sequencing technology is capable of detecting 4mC directly for any bacterial species regardless of whether an assembled genome exists or not, it is not as scalable to profiling hundreds to thousands of samples compared with the commonly used next-generation sequencing technologies. Here, we present 4mC-Tet-assisted bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that rapidly and cost efficiently reveals the genome-wide locations of 4mC for bacterial species with an available assembled reference genome. In 4mC-TAB-seq, both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out as cytosines, revealing their specific positions throughout the genome. We applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc genus, Caldicellulosiruptor, in which 4mC-related restriction is a major barrier to DNA transformation from other species. In combination with MethylC-seq, both 4mC- and 5mC-containing motifs are identified which can assist in rapid and efficient genetic engineering of these bacteria in the future.
Indexed as
Identifiers
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.