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MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation.

ABSTRACT:

Motivation

The two major epigenetic modifications of cytosines, 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), coexist with each other in a range of mammalian cell populations. Increasing evidence points to important roles of 5-hmC in demethylation of 5-mC and epigenomic regulation in development. Recently developed experimental methods allow direct single-base profiling of either 5-hmC or 5-mC. Meaningful analyses seem to require combining these experiments with bisulfite sequencing, but doing so naively produces inconsistent estimates of 5-mC or 5-hmC levels.

Results

We present a method to jointly model read counts from bisulfite sequencing, oxidative bisulfite sequencing and Tet-Assisted Bisulfite sequencing, providing simultaneous estimates of 5-hmC and 5-mC levels that are consistent across experiment types.

Availability

http://smithlab.usc.edu/software/mlml

SUBMITTER: Qu J

PROVIDER: S-EPMC3789553 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

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MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation.

Qu Jianghan J Zhou Meng M Song Qiang Q Hong Elizabeth E EE Smith Andrew D AD

Bioinformatics (Oxford, England) 20130821 20

<h4>Motivation</h4>The two major epigenetic modifications of cytosines, 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), coexist with each other in a range of mammalian cell populations. Increasing evidence points to important roles of 5-hmC in demethylation of 5-mC and epigenomic regulation in development. Recently developed experimental methods allow direct single-base profiling of either 5-hmC or 5-mC. Meaningful analyses seem to require combining these experiments with bisulfite ...[more]

PMID: 23969133

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