title: MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes.
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.
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China.
authors.forename: Shi
authors.initials: S
authors.lastname: Wang
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.
authors.forename: Jia
authors.initials: J
authors.lastname: Lv
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.
authors.forename: Jinzhuang
authors.initials: J
authors.lastname: Dou
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.
authors.forename: Xue
authors.initials: X
authors.lastname: Li
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.
authors.forename: Xiaoteng
authors.initials: X
authors.lastname: Fu
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.
authors.forename: Huaiqian
authors.initials: H
authors.lastname: Dou
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.
authors.forename: Junxia
authors.initials: J
authors.lastname: Mao
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Hu
authors.affiliation: Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China Qingdao National Laboratory for Marine Science and Technology, Qingdao, People's Republic of China zmbao@ouc.edu.cn.
authors.forename: Zhenmin
authors.initials: Z
authors.lastname: Bao
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D019175:DNA Methylation; D004262:DNA Restriction Enzymes / Q000378:metabolism; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D049897:Pectinidae / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004262:DNA Restriction Enzymes
keywords: DNA methylation; MRR-like enzyme; MethylRAD; epigenomics