Bioinformatics Seminars

Bioinformatics Seminar

Time: 10:45am Tuesdays.
Venue:
Level 7 Seminar Room 2, WEHI1

7 November 2017

Differential methylation analysis of reduced representation bisulfite sequencing experiments

Yunshun Chen
WEHI Bioinformatics

Studies in epigenetics have shown that DNA methylation is a key factor in regulating gene expression. DNA methylation typically occurs in CpG context. When located in a gene promoter, DNA methylation often acts to repress transcription and gene expression. The most commonly used technology of studying DNA methylation is bisulfite sequencing (BS-seq), which can be used to measure genome-wide methylation levels on the single-nucleotide scale. Notably, BS-seq can also be combined with enrichment strategies such as reduced representation bisulfite sequencing (RRBS) to target CpG-rich regions in order to save per-sample costs.

A typical DNA methylation analysis often involves identifying differentially methylated regions (DMRs) between different experimental conditions. Many statistical methods have been developed for finding DMRs in BS-seq data. In this talk, I will describe a novel approach of detecting DMRs using edgeR. Simulation studies have been carried out to compare our approach with existing methods. A case study will also be provided to demonstrate how differential methylation analyses can be fit into the existing pipelines specifically designed for RNA-seq differential expression studies. The method proposed in the talk can be applied to any BS-seq data that includes some replication, but it is especially appropriate for RRBS data with small numbers of biological replicates.


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