MeDIP-HMM

by Michael Seifert, Sandra Cortijo, Maria Colome-Tatche, Frank Johannes, Francois Roudier, and Vincent Colot

Description

Motivation

Methylation of cytosines in DNA is an important epigenetic mechanism involved in transcriptional regulation and preservation of genome integrity in a wide range of eukaryotes. Immunoprecipitation of methylated DNA followed by hybridization to genomic tiling arrays (MeDIP-chip) is a cost-effective and sensitive method for methylome analyses. However, existing bioinformatics methods only enable a binary classification into unmethylated and methylated genomic regions, which limits biological interpretations. Indeed, DNA methylation levels can vary substantially within a given DNA fragment depending on the number of contained methylated cytosines. Therefore, a method for the identification of more than two methylation states from MeDIP-chip data is highly desirable.

Results

Here, we present a three-state Hidden Markov Model (MeDIP-HMM) for analyzing MeDIP-chip data. MeDIP-HMM utilizes a higher-order state-transition process improving modeling of spatial dependencies between chromosomal regions, allows a simultaneous analysis of replicates, and enables a differentiation between unmethylated, methylated and highly methylated genomic regions. We train MeDIP-HMM using a Bayesian Baum-Welch algorithm integrating prior knowledge on methylation levels. We apply MeDIP-HMM to the analysis of the Arabidopsis root methylome and systematically investigate the benefit of using higher-order HMMs. Moreover, we also perform an in-depth comparison study to existing methods and demonstrate the value of using MeDIP-HMM by comparisons to current knowledge on the Arabidopsis methylome. We find that MeDIP-HMM is a fast and precise method for the analysis of DNA methylation data enabling the identification of distinct DNA methylation levels. These results suggest that MeDIP-HMM could also be useful for analyses of other methylomes.

Paper

The paper MeDIP-HMM: Genome-wide identification of distinct DNA methylation states from high-density tiling arrays has been submitted to Bioinformatics.

Download

• MeDIP-HMM: A ZIP file containing a JAR file for analyzing methylome data sets by MeDIP-HMMs and the Arabidopsis root methylome data set considered in our study.