DREAM: A Simple Method for DNA Methylation Profiling by High-throughput Sequencing

2016 ◽  
pp. 111-127 ◽  
Author(s):  
Jaroslav Jelinek ◽  
Jozef Madzo
Keyword(s):  
Dna Methylation ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Simple Method ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

scholarly journals A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling

2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Hailong Meng ◽  
Andrew R Joyce ◽  
Daniel E Adkins ◽  
Priyadarshi Basu ◽  
Yankai Jia ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Statistical Method ◽  
High Throughput ◽  
Cpg Sites ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

scholarly journals MethylRAD: a simple and scalable method for genome-wide DNA methylation profiling using methylation-dependent restriction enzymes

Open Biology ◽  
2015 ◽  
Vol 5 (11) ◽  
pp. 150130 ◽  
Author(s):  
Shi Wang ◽  
Jia Lv ◽  
Lingling Zhang ◽  
Jinzhuang Dou ◽  
Yan Sun ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Method Development ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Biological Significance ◽  
Restriction Enzymes ◽  
Phylogenetic Groups ◽  
Patinopecten Yessoensis ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

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.

Application of Microarrays for DNA Methylation Profiling

2008 ◽  
pp. 109-129 ◽  
Author(s):  
Axel Schumacher ◽  
Andreas Weinhäusl ◽  
Arturas Petronis
Keyword(s):  
Dna Methylation ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

Forensic DNA methylation profiling from minimal traces: How low can we go?

2018 ◽  
Vol 33 ◽  
pp. 17-23 ◽  
Author(s):  
Jana Naue ◽  
Huub C.J. Hoefsloot ◽  
Ate D. Kloosterman ◽  
Pernette J. Verschure
Keyword(s):  
Dna Methylation ◽  
Forensic Dna ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

scholarly journals DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome

2016 ◽  
Vol 99 (3) ◽  
pp. 555-566 ◽  
Author(s):  
Ricky S. Joshi ◽  
Paras Garg ◽  
Noah Zaitlen ◽  
Tuuli Lappalainen ◽  
Corey T. Watson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Uniparental Disomy ◽  
Dna Methylation Profiling ◽  
Methylation Profiling
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