Beadchip Technology to Detect DNA Methylation in Mouse Faithfully Recapitulates Whole-Genome Bisulfite Sequencing

Abstract

Aim: To facilitate wide-scale implementation of Illumina Mouse Methylation BeadChip (MMB) technology, array-based measurement of cytosine methylation was compared with the gold-standard assessment of DNA methylation by whole-genome bisulfite sequencing (WGBS). Methods: DNA methylation across two mouse strains (C57B6 and C3H) and both sexes was assessed using the MMB and compared with previously existing deep-coverage WGBS of mice of the same strain and sex. Results & conclusion: The findings demonstrated that 93.3–99.2% of sites had similar measurements of methylation across technologies and that differentially methylated cytosines and regions identified by each technology overlap and enrich for similar biological functions, suggesting that the MMB faithfully recapitulates the findings of WGBS.

Keywords::

• DNA methylation
• mouse methylation array
• whole-genome bisulfite sequencing

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2023-0034

Acknowledgments

We thank the National Institute of Environmental Health Science (NIEHS) Microarray Core for their support in the assessment of DNA methylation by Illumina array. We also thank Stephanie London for her critical reading of this paper.

Financial & competing interests disclosure

This work was supported by the Intramural Research Program of the National Institute of Environmental Health Science (ES101965 to PA Wade and ES103372 to EM Martin) and National Institute of General Medical Sciences Postdoctoral Research Associate Training Program (Fi2GM133546 to EM Martin). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

Animal housing and procedures were approved by the Institutional Animal Care and Use Committee of NIEHS and follow the recommendations of the Guide for the Care and Use of Laboratory Animals.

Data sharing

The whole-genome bisulfite sequencing and array data discussed in this publication have been deposited in the Gene Expression Omnibus (accession number: GSE106379, GSE106208, GSE228602).

Additional information

Funding

This work was supported by the Intramural Research Program of the National Institute of Environmental Health Science (ES101965 to PA Wade and ES103372 to EM Martin) and National Institute of General Medical Sciences Postdoctoral Research Associate Training Program (Fi2GM133546 to EM Martin). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.