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Hypothesis and Theory ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00801

A Novel Application of Mixed Effects Models for Reconciling Base-Pair Resolution 5-methylcytosine and 5-hydroxymethylcytosine Data in Neuroepigenetics

  • 1Translational Science and Molecular Medicine, College of Human Medicine, Michigan State University, United States

Epigenetic marks operate at multiple chromosomal levels to regulate gene expression, from direct covalent modification of DNA to 3D chromosomal structure. Research has shown that 5-methylcytosine (5-mC) and its oxidized form, 5-hydroxymethylcytosine (5-hmC), are stable epigenetic marks with distinct genomic distributions and separate regulatory functions. In addition, recent data indicate that 5-hmC plays a critical regulatory role in the mammalian brain, emphasizing the importance of considering this alternative DNA modification in the context of neuroepigenetics. Traditional bisulfite (BS) treatment-based methods to measure the methylome are not able to distinguish between 5-mC and 5-hmC, meaning much of the existing literature does not differentiate these two DNA modifications. Recently developed methods, including Tet-assisted bisulfite (TAB) treatment and oxidative bisulfite (oxBS) treatment, allow for differentiation of 5-hmC and/or 5-mC levels at base-pair resolution when combined with next-generation sequencing or methylation arrays. Despite these technological advances, there remains a lack of clarity regarding the appropriate statistical methods for integration of 5-mC and 5-hmC data. As a result, it can be difficult to determine the effects of an experimental treatment on 5-mC and 5-hmC dynamics. Here, we propose a statistical approach involving generalized linear mixed effects to simultaneously model paired 5-mC and 5-hmC data as repeated measures. We tested this approach using publicly available BS/oxBS-450K array data, and showed that our new approach detected far more CpG probes with paired changes in 5-mC and 5-hmC by Alzheimer’s disease status (n=14183 probes) compared to the overlapping differential probes generated from separate models for each epigenetic mark (n=68). Of note, all 68 of the overlapping probe IDs from the separate models were also significant in our new modeling approach, supporting the sensitivity of our new analysis method. Using the proposed approach, it will be possible to determine the effects of an experimental treatment on both 5-mC and 5-hmC at the base-pair level.

Keywords: neuroepigenetics, Mixed effects model for repeated measures, 5-Methylcytosine, 5-Hydroxymethylcytosine, bioinformatics

Received: 08 May 2019; Accepted: 31 Jul 2019.

Edited by:

Douglas M. Ruden, Wayne State University, United States

Reviewed by:

Pao-Yang Chen, Institute of Plant and Microbial Biology, Academia Sinica, Taiwan
Li Chen, Auburn University, United States  

Copyright: © 2019 Kochmanski, Savonen and Bernstein. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: PhD. Alison I. Bernstein, Translational Science and Molecular Medicine, College of Human Medicine, Michigan State University, East Lansing, 49503, Michigan, United States, Alison.Bernstein@hc.msu.edu