Research Article: A complex association between DNA methylation and gene expression in human placenta at first and third trimesters

Date Published: July 13, 2017

Publisher: Public Library of Science

Author(s): Yen Ching Lim, Jie Li, Yiyun Ni, Qi Liang, Junjiao Zhang, George S. H. Yeo, Jianxin Lyu, Shengnan Jin, Chunming Ding, Dajun Deng.


The human placenta is a maternal-fetal organ essential for normal fetal development and maternal health. During pregnancy, the placenta undergoes many structural and functional changes in response to fetal needs and environmental exposures. Previous studies have demonstrated widespread epigenetic and gene expression changes from early to late pregnancy. However, on the global level, how DNA methylation changes impact on gene expression in human placenta is not yet well understood. We performed DNA methylome analysis by reduced representation bisulfite sequencing (RRBS) and gene expression analysis by RNA-Seq for both first and third trimester human placenta tissues. From first to third trimester, 199 promoters (corresponding to 189 genes) and 2,297 gene bodies were differentially methylated, with a clear dominance of hypermethylation (96.8% and 93.0% for promoters and gene bodies, respectively). A total of 2,447 genes were differentially expressed, of which 77.2% were down-regulated. Gene ontology analysis using differentially expressed genes were enriched for cell cycle and immune response functions. The correlation between DNA methylation and gene expression was non-linear and complex, depending on the genomic context (promoter or gene body) and gene expression levels. A wide range of DNA methylation and gene expression changes were observed at different gestational ages. The non-linear association between DNA methylation and gene expression indicates that epigenetic regulation of placenta development is more complex than previously envisioned.

Partial Text

The human placenta is a temporary maternal-fetal organ essential for normal fetal development. It serves several functions such as exchange of oxygen, nutrients and waste products between the mother and fetus. During pregnancy, the human placenta undergoes tremendous changes in size, morphology and structure to cope with the development of the fetus [1–3].

Using an improved method of reduced representation bisulfite sequencing (RRBS) [19,21], we quantified DNA methylation of six first trimester and five third trimester placenta villi samples. Using a minimum sequencing depth of 10 as the cutoff, we obtained on average 1.8 million CpGs per sample (S1 Table and S1 Fig). To facilitate cross gestation comparison, we further removed CpG sites that were on the sex chromosomes or present in less than three samples in either the first or the third trimester group, resulting in 1.7 million CpG sites for further analysis. These CpGs represented about 3% of Hg19 autosomal CpGs, 78% of CGIs, 70.8% of core promoters (defined as -1kb upstream and +500bp downstream from a transcription start site) and 64.2% of gene bodies (defined as +1kb downstream from a transcription start site to the transcription termination site).

In this study, we applied next generation sequencing techniques to study the gene expression (by RNA-Seq) and DNA methylation profiles (by RRBS) of human placenta tissues derived from early and late gestations.




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