ArticleOpen biology2015
MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes.
Article in Open biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 111 citations in OpenAlex.
- Whole genome DNA methylation atlas of the scallop Patinopecten yessoensis.Scientific data · 2026Article
- Article
- Inverse Restriction Site-Associated DNA Sequencing (iRAD-seq).Bio-protocol · 2026Article
- Article
- Prior exposure to hypoxia alters DNA methylation patterns in the eastern oyster.bioRxiv : the preprint server for biology · 2025Article
- Advancements in DNA methylation technologies and their application in cancer diagnosis.Epigenetics · 2025Review
- The dynamic epigenetic atlas and its effects on instability of starch and seed storage protein quality traits in wheat (Frontiers in plant science · 2025Article
- Genome-wide DNA methylation and transcriptome sequencing analyses of lens tissue in an age-related mouse cataract model.PloS one · 2025Article
- Chloroplast DNA methylation in the kelpEvolutionary applications · 2024Article
- Detection of DNA methylation signatures through the lens of genomic imprinting.Scientific reports · 2024Article
- Machine Learning Analysis of the Impact of Silver Nitrate and Silver Nanoparticles on Wheat (Plants (Basel, Switzerland) · 2023Article
- Differences by origin in methylome suggest eco-phenotypes in the kelpEvolutionary applications · 2023Article
- Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii.Nature communications · 2022Article
- Effects of Zinc, Copper and Iron Oxide Nanoparticles on Induced DNA Methylation, Genomic Instability and LTR Retrotransposon Polymorphism in Wheat (Plants (Basel, Switzerland) · 2022Article
- Epigenomic insight of lingonberry and health-promoting traits during micropropagation.Scientific reports · 2022Article
- DNA Methylation Difference between Female and Male Ussuri Catfish (Life (Basel, Switzerland) · 2022Article
- Heterosis and Differential DNA Methylation in Soybean Hybrids and Their Parental Lines.Plants (Basel, Switzerland) · 2022Article
- Changes in gene body methylation do not correlate with changes in gene expression in Anthozoa or Hexapoda.BMC genomics · 2022Article
- Effects of Cryopreservation on Sperm with Cryodiluent in Viviparous Black Rockfish (International journal of molecular sciences · 2022Article
- Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M.Genome biology · 2022Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Characterization of dynamic DNA methylomes in diverse phylogenetic groups has attracted growing interest for a better understanding of the evolution of DNA methylation as well as its function and biological significance in eukaryotes. Sequencing-based methods are promising in fulfilling this task. However, none of the currently available methods offers the 'perfect solution', and they have limitations that prevent their application in the less studied phylogenetic groups. The recently discovered Mrr-like enzymes are appealing for new method development, owing to their ability to collect 32-bp methylated DNA fragments from the whole genome for high-throughput sequencing. Here, we have developed a simple and scalable DNA methylation profiling method (called MethylRAD) using Mrr-like enzymes. MethylRAD allows for de novo (reference-free) methylation analysis, extremely low DNA input (e.g. 1 ng) and adjustment of tag density, all of which are still unattainable for most widely used methylation profiling methods such as RRBS and MeDIP. We performed extensive analyses to validate the power and accuracy of our method in both model (plant Arabidopsis thaliana) and non-model (scallop Patinopecten yessoensis) species. We further demonstrated its great utility in identification of a gene (LPCAT1) that is potentially crucial for carotenoid accumulation in scallop adductor muscle. MethylRAD has several advantages over existing tools and fills a void in the current epigenomic toolkit by providing a universal tool that can be used for diverse research applications, e.g. from model to non-model species, from ordinary to precious samples and from small to large genomes, but at an affordable cost.
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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.