DNA methylation subpatterns at distinct regulatory regions in human early embryos.

Rongsong Luo,Guanghua Su,Zhong Zheng,Guangpeng Li,Guangqi Gao,Yongchun Zuo,Chunling Bai,Lei Yang,Zhuying Wei

doi:10.1098/rsob.180131

Abstract

DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell- and single-base-resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic development. In this study, the region from upstream 20 kb to downstream 20 kb of RefSeq gene was selected and divided into 12 distinct regions (up20, up10, up5, up2, 5'UTR, exon, intron, 3'UTR, down2, down5, down10 and down20). The candidate promoter region (TSS ± 2 kb) was further divided into 20 consecutive subregions, which were termed ‘bins’. The DNA methylation dynamics of these regions were systematically analysed along with their effects on gene expression in human early embryos. The dynamic DNA methylation subpatterns at the distinct genomic regions with a focus on promoter regions were mapped. For the 12 distinct genomic regions, up2 and 5'UTR had the lowest DNA methylation levels, and their methylation dynamics were different with other regions. The region 3'UTR had the highest DNA methylation levels, and the correlation analysis with gene expression proved that it was a feature of transcribed genes. For the 20 bins in promoter region, the CpG densities showed a normal distribution pattern, and the trend of the methylated CpG counts was inverse with the DNA methylation levels, especially for the bin 1 (downstream 200 bp of the TSS). Through the correlation analysis between DNA methylation and gene expression, the current study finally revealed that the region bin −4 to 6 (800 bp upstream to 1200 bp downstream of the TSS) was the best candidate for the promoter region in human early embryos, and bin 1 was the putative key regulator of gene activity. This study provided a global and high-resolution view of DNA methylation subpatterns at the distinct genomic regions in human early embryos.

Highlights

In mammalian reproduction, a sperm fertilizes an egg, and the zygote undergoes cleavage and develops into a morula; the inner cells of the morula give rise to the inner cell mass (ICM), from which the embryo proper is derived, whereas the outer cells differentiate into the trophectoderm (TE), which gives rise to extraembryonic tissues [1]
This study provided a highresolution and global view of DNA methylation subpatterns at the distinct genomic regions in human early embryos
We performed an integrated analysis between DNA methylation at distinct genomic regions and gene expression in human early embryos, and mapped DNA methylation patterns at these distinct genomic regions

Summary

Introduction

A sperm fertilizes an egg, and the zygote undergoes cleavage and develops into a morula; the inner cells of the morula give rise to the inner cell mass (ICM), from which the embryo proper is derived, whereas the outer cells differentiate into the trophectoderm (TE), which gives rise to extraembryonic tissues [1] This developmental process requires extensive erasure of epigenetic marks, and the dynamics of pre-implantation are driven by the need to reprogram haploid parental epigenomes for the morula to reach a totipotent state in which epigenetic programmes essential for the first-cell lineage commitment and differentiation are established. Remethylation occurs gradually until the original levels are reached [13,14]

Methods

Results

Conclusion