DNA Methylation Landscapes of Human Fetal Development

Abstract

Remodelling the methylome is a hallmark of mammalian development and cell differentiation. However, current knowledge of DNA methylation dynamics in human tissue specification and organ development largely stems from the extrapolation of studies in vitro and animal models. Here, we report on the DNA methylation landscape using the 450k array of four human tissues (amnion, muscle, adrenal and pancreas) during the first and second trimester of gestation (9,18 and 22 weeks). We show that a tissue-specific signature, constituted by tissue-specific hypomethylated CpG sites, was already present at 9 weeks of gestation (W9). Furthermore, we report large-scale remodelling of DNA methylation from W9 to W22. Gain of DNA methylation preferentially occurred near genes involved in general developmental processes, whereas loss of DNA methylation mapped to genes with tissue-specific functions. Dynamic DNA methylation was associated with enhancers, but not promoters. Comparison of our data with external fetal adrenal, brain and liver revealed striking similarities in the trajectory of DNA methylation during fetal development. The analysis of gene expression data indicated that dynamic DNA methylation was associated with the progressive repression of developmental programs and the activation of genes involved in tissue-specific processes. The DNA methylation landscape of human fetal development provides insight into regulatory elements that guide tissue specification and lead to organ functionality.

Fig 1. Tissue- and time-specific DNA methylation patterns during human fetal development.

(A) Clustering based on Euclidean distance. (B) Multidimensional scaling based on Euclidean distance of the four tissues. (C) Median DNA methylation for each of the four tissues over time with a combined genic and CGI-centric annotation. CGI, CpG island.

Fig 2. Sets of hypomethylated CpG sites are tissue-specific.

(A) Heatmap representing hypomethylated CpGs per tissue, defined by a beta difference of ≥ 0.2 of the studied tissue compared to the other tissues. (B) Combined genic and CGI-centric annotation for the hypomethylated CpGs per tissue represented as the odds ratio (see S3A Fig for odds ratios). CGI, CpG island; DP, distal promoter; DS, downstream; GB, gene body; IG, intergenic; NC, non-CGI; PP, proximal promoter; SHE, shelves; SHO, shores. (C) Enrichment of hypomethylated CpGs in the chromatin state segmentation states for the matching tissues (amnion, fetal muscle, fetal adrenal and adult pancreatic islets; see S3B Fig for odds ratios).

Fig 3. Gain and loss of DNA methylation during human fetal development.

(A) Heatmap of CpGs with a gain and a loss, respectively, of methylation over time. Gain and loss of methylation was defined as a difference of beta ≥ 0.2 between W9 and W22, and W18 in between. (B) Mean methylation of CpGs with a gain or loss of DNA methylation for fetal tissues and their adult counterpart. (C) Combined genic and CGI-centric annotation for CpGs with a gain or a loss of methylation represented as the odds ratio (see S4B Fig for odds ratios). CGI, CpG island; DP, distal promoter; DS, downstream; GB, gene body; IG, intergenic; NC, non-CGI; PP, proximal promoter; SHE, shelves; SHO, shores. (D) Enrichment of dynamically methylated CpGs in the chromatin segmentation states for the matching tissues (fetal muscle, fetal adrenal, amnion and adult pancreatic islets; see S4C Fig for odds ratios).

Fig 4. DNA methylation dynamics are accompanied by changes in gene expression.

(A) Expression profiles of genes in embryonic morphogenesis near dynamic regions with gain of methylation represented as median with the interquartile range (IQR) [40]. (B) Expression profiles of genes near dynamic regions with loss of methylation grouped by significant, tissue-specific Gene Ontology terms for each of the four tissues from S3 Table represented as median with IQR [40]. Reg., regulation.

Fig 5. Association of gain and loss of DNA methylation, DNAse I hypersensitive sites and histone modifications.

(A) Venn diagram visualizing the overlaps between genes with a gain and a loss of methylation of the three embryonic tissues. (B) Methylation difference between W9 and W22 of MYLK2 in the four tissues. (C) Methylation difference between W9 and W22 of the HOXB cluster. (D) Mean DNAse I hypersensitive (DHS) and histone modifications signals in a 5 kb flanking region of the muscle dDMRs in HSMMs and HSMMtubes. HSMM, human skeletal muscle myoblasts; HSMMtube, human skeletal muscle myotubes.

Fig 6. DNA methylation dynamics during human development.

This illustration depicts the current comprehensive knowledge of DNA methylation during human pre- and postimplantation development. The knowledge about DNA methylation during human preimplantation (left panel) is derived from [–12] whereas our study sheds light on postimplantation development (right panel).