title: An integrated platform for bovine DNA methylome analysis suitable for small samples.
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.
authors.forename: Habib A
authors.initials: HA
authors.lastname: Shojaei Saadi
authors.forename: Alan M
authors.initials: AM
authors.lastname: O'Doherty
authors.forename: Dominic
authors.initials: D
authors.lastname: Gagné
authors.forename: Éric
authors.initials: É
authors.lastname: Fournier
authors.forename: Jason R
authors.initials: JR
authors.lastname: Grant
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Sirard
authors.affiliation: 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. claude.robert@fsaa.ulaval.ca.
authors.forename: Claude
authors.initials: C
authors.lastname: Robert
mesh_terms: D000818:Animals; D001755:Blastocyst / Q000378:metabolism; D002417:Cattle; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D018392:Genomic Imprinting; D023281:Genomics / Q000379:methods; D008297:Male; D015203:Reproducibility of Results; D013094:Spermatozoa / Q000378:metabolism; D059467:Transcriptome; D064878:Web Browser