Validation of a DNA methylation microarray for 285,000 CpG sites in the mouse genome.

Content Provider	Europe PMC
Author	Garcia-Prieto, Carlos A. Álvarez-Errico, Damiana Musulen, Eva Bueno-Costa, Alberto N. Vazquez, Berta Vaquero, Alejandro Esteller, Manel
Copyright Year	2022
Abstract	ABSTRACTMouse has been extensively used as a model organism in many studies to characterize biological pathways and drug effects and to mimic human diseases. Similar DNA sequences between both species facilitate these types of experiments. However, much less is known about the mouse epigenome, particularly for DNA methylation. Progress in delivering mouse DNA methylomes has been slow due to the currently available time-consuming and expensive methodologies. Following the great acceptance of the human DNA methylation microarrays, we have herein validated a newly developed DNA methylation microarray (Infinium Mouse Methylation BeadChip) that interrogates 280,754 unique CpG sites within the mouse genome. The CpGs included in the platform cover CpG Islands, shores, shelves and open sea sequences, and loci surrounding transcription start sites and gene bodies. From a functional standpoint, mouse ENCODE representative DNase hypersensitivity sites (rDHSs) and candidate cis-Regulatory Elements (cCREs) are also included. Herein, we show that the profiled mouse DNA methylation microarray provides reliable values among technical replicates; matched results from fresh frozen versus formalin-fixed samples; detects hemimethylated X-chromosome and imprinted CpG sites; and is able to determine CpG methylation changes in mouse cell lines treated with a DNA demethylating agent or upon genetic disruption of a DNA methyltransferase. Most important, using unsupervised hierarchical clustering and t-SNE approaches, the platform is able to classify all types of normal mouse tissues and organs. These data underscore the great features of the assessed microarray to obtain comprehensive DNA methylation profiles of the mouse genome.
Related Links	https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC9621044&blobtype=pdf
Page Count	9
ISSN	15592294
Journal	Epigenetics
Volume Number	17
DOI	10.1080/15592294.2022.2053816
PubMed Central reference number	PMC9621044
Issue Number	12
PubMed reference number	35297293
e-ISSN	15592308
Language	English
Publisher	Taylor & Francis
Publisher Date	2022-03-21
Access Restriction	Open
Rights License	This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way. © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
Subject Keyword	Mouse DNA methylation microarray epigenetics CpG sites validation
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Cancer Research