The second chapter discusses how DNA bisulfite treatment together with high-throughput sequencing allows determining the DNA methylation on a whole genome scale at single cytosine resolution and introduces software for analysis of bisulfite sequencing data. The third chapter presents analysis of GC3-rich genes that have more methylation targets. The fourth chapter is dedicated to inheritance of DNA methylation in plant genomes and introduces restriction landmark genome scanning method - a quantitative approach for simultaneous assay of methylation status and the fifth chapter presents MethylMeter, a new bisulfite-free method to detect and quantify DNA methylation is described and applied to the detection of imprinting disorders
