Genome-Wide Epigenetic Characterization of Tissues from Three Germ Layers Isolated from Sheep Fetuses.

Emanuele Capra,Pasqualino Loi,Paola Toschi,Alessandra Stella,John L Williams,Barbara Lazzari,Marcello Del Corvo,Pier A Scapolo,Paolo Ajmone-Marsan

doi:10.3389/fgene.2017.00115

Abstract

DNA methylation of regulatory and growth-related genes contributes to fetal programming which is important for maintaining the correct development of three germ layers of the embryo that develope into different tissues and organs, and which persists into adult life. In this study, a preliminary epigenetic screen was performed to define genomic regions that are involved in fetal epigenome remodeling. Embryonic ectodermic tissues (origin of nervous tissue), mesenchymal tissues (origin of connective and muscular tissues), and foregut endoderm tissues (origin of epithelial tissue), from day 28 sheep fetuses were collected and the distribution of methylated CpGs was analyzed using whole-genome bisulfite sequencing. Patterns of methylation among the three tissues showed a high level of conservation of hypo-methylated CpG islands CGIs, and a consistent level of methylation in regulatory genetic elements. Analysis of tissue specific differentially methylated regions, revealed that 20% of the total CGIs differed between tissues. A proportion of the methylome was remodeled in gene bodies, 5′ UTRs and 3′ UTRs (7, 11, and 11%, respectively). Genes with overlapping differentially methylated regions in gene bodies and CGIs showed a significant enrichment for tissue morphogenesis and development pathways. The data presented here provides a “reference” for the epigenetic status of genes potentially involved in the maintenance and regulation of fetal developmental during early life, a period expected to be particularly prone to epigenetic alterations induced by environmental and nutritional stressors.

Highlights

Methylation of CpG dinucleotides in the mammalian genome is a heritable epigenetic mark and serves as an important mediator between the environment and genome function
CpG methylation at 1,459 Methylated regions (MRs) located in CpG islands (CGIs) was examined in the three tissues: EC had 870 MRs, M 868 MRs and EN 915 MRs with low CpG methylation status
Transcription start sites (TSSs) differed in hypomethylated versus hypermethylated CGIs regions: hypo-methylated regions were enriched in TSS elements and clearly positioned within a few 100 bp of TSSs, whereas TSSs were poor in hyper-methylated CGI and distributed over more distal positions (Supplementary Table S2 and Figure S2)

Summary

Introduction

Methylation of CpG dinucleotides in the mammalian genome is a heritable epigenetic mark and serves as an important mediator between the environment and genome function. DNA methylation of cytosine residues, at CpG dinucleotides, has been identified as an important regulatory mechanism of genome. During mammalian development the DNA methylome is extensively remodeled in different cell lineages during differentiation. These dynamic changes lead to unique DNA methylation signatures in adult tissues, consistent with cell lineage and function (Reik et al, 2001; Bird, 2002; Smith and Meissner, 2013; Messerschmidt et al, 2014). The level of methylation of these regions declines in adult tissues following an active demethylation wave during growth which continues gradually with aging

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Discussion

Conclusion