Abstract
Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation. Methyl groups can be covalently bound to the carbon-5 of cytosines or the carbon-6 of adenine bases. DNA methylation can be found in both prokaryotes and eukaryotes. In the latter, dynamic variation is shown across species, along development, and by cell type. DNA methylation usually leads to a lower binding affinity of DNA-interacting proteins and often results in a lower expression rate of the subsequent genome region, a process also referred to as transcriptional gene silencing. We give an overview of the current state of research facilitating the planning and implementation of whole-genome bisulfite-sequencing (WGBS) experiments. We refrain from discussing alternative methods for DNA methylation analysis, such as reduced representation bisulfite sequencing (rrBS) and methylated DNA immunoprecipitation sequencing (MeDIPSeq), which have value in specific experimental contexts but are generally disadvantageous compared to WGBS.
Highlights
Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation [1]
Methylated DNA immunoprecipitation sequencing (MeDIPSeq), which have value in specific experimental contexts but are generally disadvantageous compared to whole-genome bisulfite-sequencing (WGBS)
For WGBS libraries, this technique is not recommended, as a higher
Summary
Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation [1]. Whole genome bisulfite-sequencing has become the gold standard to detect DNA methylation patterns because of its single-base resolution and the possibility to cover entire genomes. During thethe bisulfite reaction of of unmethylated cytosine is converted to uracil This occurrs via cytosinsulfonate, a DNA, unmethylated cytosine is converted to uracil. Figure bisulfite-mediated conversion of of cytosine to uracil. Methylated cytosine is not affected byin bisulfite, whereas unmethylated converted to to uracil during. Plant genomes have additional CHG and CHH methylation (H = adenine, thymine or cytosine). CHG and methylation (H adenine, thymine ortwo cytosine) These two correlate with the suppression ofadenine, transposon activity [17], mobile genetic elements that canlast change their transposon activity [17],ofmobile genetic elements can genetic change elements their position within the genome. We will give a brief overview of WGBS experiment planning by discussing different types of WGBS library preparation protocols, options for sequencing technology, and bioinformatics data analysis
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