An epigenetic platform to study global DNA methylome and transcriptome in parallel from limited tissue such as early embryo
Recent technological advances and the exponential growth of the field of epigenetics, in particular genome-wide studies, are advancing our knowledge and providing more evidence for the interdependence of epigenetic and genetic variations. The importance of genome-wide epigenetic reprogramming in mammalian germ cells and early embryos has shed light on the pivotal role of epigenetics in modulating genome functions at these critical stages of development. Early embryo development is now considered to be a window of susceptibility to epigenetic reprogramming errors or dysregulation. Therefore, genome-wide profiling of early embryo epigenetics could explain the inﬂuence of factors such as the nutritional/metabolic status of the mother or the artiﬁcial environment of assisted reproductive technologies (ART). However, the peculiar nature of early embryos, in addition to their scarcity (extremely limited quantities of biological sample), poses formidable technical challenges to study the epigenetic profile of early embryo at a genome-wide scale 1.
Recently, we developed a technological platform called EmbryoGene DNA methylation analysis (EDMA) that is complementary to existing platforms such as RRBS 2. The required sample size for EDMA is as minimum as 10 ng of gDNA input (corresponding to a pool of 10 expanded blastocysts or 1,500 cells). Simultaneous extraction of the gDNA and the total RNA from the given sample, make it feasible for parallel analysis of the DNA methylome and transcriptome of early embryo using EDMA and our custom-designed transcriptome array. By providing a genome-wide parallel survey of the DNA methylome and the transcriptome for the same sample, EDMA offers a powerful tool for revealing highly relevant targets and potential associations between the DNA methylation and the transcript abundance.
In addition, we designed a user-friendly and comprehensive bioinformatics data analysis pipeline to sort the data according to defined structural characteristics (e.g. near known genes, within gene body components, distance from CpG islands, repetitive elements). This pipeline enables the identification of alterations of DNA methylation in bovine genomic regions, under various enrichment outputs in parallel to deviations in transcript abundance through generating a series of visualization tools. As a proof of concept, the DNA methylome profile of Bovine sperm and blastocysts were compared. Similar to the other studied species such as mouse, hypermethylation of bovine sperm DNA, compared to the early embryo genome, was observed and was distributed across various classes of bovine sperm genomic features.
EDMA provides a unified and reliable approach to analyze small amounts of genomic DNA, and offers a good balance between genomic coverage and data turnaround time. The built-in data analysis pipeline provides efficient means for data interpretation and represents a good option for researchers with limited bioinformatics resources. The platform is, at the present time, specific for the bovine genome – as the superior model for investigating early human development – but a similar approach could be adapted easily to any species of which the entire genome is known. Such platforms enable the study of the potential epigenetic risks associated with assisted reproductive technologies (ART) and are able to highlight the sequence of events occurring during the establishment of embryonic cell lines.
1. McGraw S, Shojaei Saadi HA, & Robert C (2013). Meeting the methodological challenges in molecular mapping of the embryonic epigenome. Molecular human reproduction, 19 (12), 809-27 PMID: 23783346
2. Shojaei Saadi HA, O’Doherty AM, Gagné D, Fournier E, Grant JR, Sirard MA, & Robert C (2014). An integrated platform for bovine DNA methylome analysis suitable for small samples. BMC genomics, 15 PMID: 24912542