Introduction

Hands-on Training in Methylation Sequencing Analysis

I-Hsuan Lin

National Yang-Ming University, Taipei, Taiwan

The materials was prepared for a NRPB workshop (Hands-On Training in Methylation Sequencing Analysis) and presented on 19th Dec 2014 at National Yang-Ming University.

DNA methylation refers to the addition of a methyl group (-CH3) to the carbon atom on cytosine or to a nitrogen atom on adenine. Typical DNA methylation occurs at a cytosine base located 5’ to a guanosine (i.e. CpG dinucleotide). Approximately 70% of the CpGs in the mammalian genome are methylated. However, dense clusters of CpG sites (known as CpG islands or CGI) are often un-methylated and found near transcriptional start sites (TSSs). The establishment, maintenance and erasing of cytosine methylation at regulatory regions can result in the modulation of gene expression, thus is one of the key epigenetic regulatory processes during development and disease.

Whole genome bisulfite sequencing (WGBS) is a high-throughput method that allows researchers to determine the pattern of DNA methylation across the entire genome. In Part 1 of this workshop, we demonstrated how to use the MethPipe methylation analysis pipeline to perform methylation calling at each CpG site and to identify HMRs (short hypomethylated regions) and PMDs (large partially methylated domains). In this session, we will show you how to make use of open source tools and data from public databases in the analysis of BS-seq data.

Update: (Apr 2020) Migrate to the new Gitbook site, broken links/images fixed

License

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