Global DNA hypermethylation in down syndrome placenta - PubMed (original) (raw)

Global DNA hypermethylation in down syndrome placenta

Shengnan Jin et al. PLoS Genet. 2013 Jun.

Abstract

Down syndrome (DS), commonly caused by an extra copy of chromosome 21 (chr21), occurs in approximately one out of 700 live births. Precisely how an extra chr21 causes over 80 clinically defined phenotypes is not yet clear. Reduced representation bisulfite sequencing (RRBS) analysis at single base resolution revealed DNA hypermethylation in all autosomes in DS samples. We hypothesize that such global hypermethylation may be mediated by down-regulation of TET family genes involved in DNA demethylation, and down-regulation of REST/NRSF involved in transcriptional and epigenetic regulation. Genes located on chr21 were up-regulated by an average of 53% in DS compared to normal villi, while genes with promoter hypermethylation were modestly down-regulated. DNA methylation perturbation was conserved in DS placenta villi and in adult DS peripheral blood leukocytes, and enriched for genes known to be causally associated with DS phenotypes. Our data suggest that global epigenetic changes may occur early in development and contribute to DS phenotypes.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Coverage of CpGs for RRBS analysis.

(A) A CpG site was considered covered if the sequencing depth was ≥10. A genomic region (CGI, CGI shore or promoter) was considered covered if at least 3 CpGs within the region was sequenced at a depth ≥10. (B) Distributions of covered CpGs in different functional regions. CGIs: CpG islands.

Figure 2

Figure 2. DNA methylation perturbations in DS.

(A) Probability density function (PDF) distribution for methylation difference between DS and normal samples for individual CpGs. Similarly, the methylation difference values for (B) 18,939 CGIs (each CGI with at least 6 covered CpGs), (C) 19,479 promoters (each promoter with at least 6 covered CpGs), (D) 30,648 gene bodies (each gene body with at least 6 covered CpGs), (E) 3,215 TTRs (each TTR with at least 6 covered CpGs) and (F) 8,611 intergenic regions (each intergenic region with at least 6 covered CpGs) were used for calculating their respective PDF distributions. In (A–F), hypermethylation in DS (DS>Normal) occurs much more frequently than hypomethylation in DS (Normal>DS). (G) Percentages of hyper- and hypomethylated CpGs in each autosome. (H) Average CGI methylation was higher in DS than in normal samples (p<0.002, Wilcoxon rank-sum test, two-sided). Only CGIs with at least 6 covered CpGs were included. (I) PDF distributions of methylation difference for all promoters and promoters targeted by REST.

Figure 3

Figure 3. Gene expression changes in DS.

For each gene, average expression values (RPKM) were calculated for both normal and DS samples. Only genes with RPKM ≥0.5 in at least one sample group were used for further analysis. Gene expression changes in DS were represented by log2 (Average DS samples expression/Average normal samples expression). (A) PDF distribution for gene expression changes for all genes, chr21 genes, hypermethylated genes and REST target genes. Genes located on chr21 were up-regulated by an average of 53% in DS. The hypermethylated genes were down-regulated, as evidenced by a left shift of the PDF curve (p<0.05, Wilcoxon rank-sum test, two-sided). The genes targeted by REST were marginally up-regulated (p = 0.06, Wilcoxon rank-sum test, two-sided). (B) Repression of gene expression by promoter hypermethylation was more prominent in promoters that were originally at lower methylation levels in normal samples. Each data point represents one hypermethylated promoter. X axis is the average methylation level in the normal samples for each promoter. Y axis is the gene expression ratio between DS and normal (log2 transformed).

Figure 4

Figure 4. A model for epigenetic contributions to DS phenotypes.

(A) Epigenetic perturbations such as global DNA methylation are early events in development. Consequently, multiple different adult tissues may share common patterns of epigenetic perturbations. Such early perturbations in response to an extra chr21 may confer certain survival advantages, at the expense of some normal developmental processes, which may lead to elevated disease risks. Further epigenetic perturbations and other abnormalities may alter cellular processes and development. Collectively, these perturbations may help contribution to many DS phenotypes with different penetrance and expressivity. Hypermethylation in DS may be caused by (B) down-regulation of the TET family genes and (C) down-regulation of REST by DYRK1A located on chr21.

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