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Open Access Methodology article

An integrated platform for bovine DNA methylome analysis suitable for small samples

Habib A Shojaei Saadi1, Alan M O’Doherty2, Dominic Gagné1, Éric Fournier1, Jason R Grant3, Marc-André Sirard1 and Claude Robert1*

Author Affiliations

1 Laboratory of Functional Genomics of Early Embryonic Development, Institut des nutraceutiques et des aliments fonctionnels, Faculté des sciences de l’agriculture et de l’alimentation, Pavillon des services, Université Laval, Québec G1V 0A6, Canada

2 School of Agriculture, Food Science & Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland

3 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada

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BMC Genomics 2014, 15:451  doi:10.1186/1471-2164-15-451

Published: 9 June 2014

Abstract

Background

Oocytes and early embryos contain minute amounts of DNA, RNA and proteins, making the study of early mammalian development highly challenging. The study of the embryo epigenome, in particular the DNA methylome, has been made accessible thanks to the possibility of amplifying specific sequences according to their initial methylation status. This paper describes a novel platform dedicated to the genome-wide study of bovine DNA methylation, including a complete pipeline for data analysis and visualization. The platform allows processing and integrating of DNA methylome and transcriptome data from the same sample. Procedures were optimized for genome-wide analysis of 10 ng of DNA (10 bovine blastocysts). Bovine sperm and blastocysts were compared as a test of platform capability.

Results

The hypermethylation of bovine sperm DNA compared to the embryo genome was confirmed. Differentially methylated regions were distributed across various classes of bovine sperm genomic feature including primarily promoter, intronic and exonic regions, non-CpG-island regions (shore, shelf and open-sea) and CpG islands with low-to-intermediate CpG density. The blastocyst genome bore more methylation marks than sperm DNA only in CpG islands with high CpG density. Long-terminal-repeat retrotransposons (LTR), LINE and SINE were more methylated in sperm DNA, as were low-complexity repetitive elements in blastocysts.

Conclusions

This is the first early embryo compatible genome-wide epigenetics platform for bovine. Such platforms should improve the study of the potential epigenetic risks of assisted reproductive technologies (ART), the establishment sequence of embryonic cell lines and potential deviations in both gene expression and DNA methylation capable of having long-term impact.

Keywords:
Epigenome; DNA methylation; Bovine embryo; Methylome and transcriptome parallel analysis; Analysis pipeline; CpG enrichment; Repetitive elements; Epigenome-wide association study