A Bayesian framework for genome-wide inference of DNA methylation levels

Abstract

DNA methylation is an important epigenetic mark that has been studied extensively for its regulatory role in biological processes and diseases. WGBS allows for genome-wide measurements of DNA methylation up to single-base resolutions, yet poses challenges in identifying significantly different methylation patterns across distinct biological conditions. We propose a novel methylome change-point model which describes the joint dynamics of methylation regimes of a case and a control group and benefits from taking into account the information of neighbouring methylation sites among all available samples. We also devise particle filtering and smoothing algorithms to perform efficient inference of the latent methylation patterns. We illustrate that our approach can detect and test for very flexible differential methylation signatures with high power while controlling Type-I error measures.