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Global DNA Hypermethylation in Down Syndrome Placenta

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Chunming Ding

PROVIDER: E-GEOD-42144 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global DNA hypermethylation in down syndrome placenta.

Jin Shengnan S Lee Yew Kok YK Lim Yen Ching YC Zheng Zejun Z Lin Xueqin Michelle XM Ng Desmond P Y DP Holbrook Joanna D JD Law Hai Yang HY Kwek Kenneth Y C KY Yeo George S H GS Ding Chunming C

PLoS genetics 20130606 6

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 demethyla ...[more]

PMID: 23754950

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Global DNA Hypermethylation in Down Syndrome Placenta [Bisulfite-Seq]

Project description:We have performed genome-wide DNA methylation analysis at single base resolution and gene expression analysis, resulted in hypermethylation in all autosomes in DS samples, mediated by down-regulation of all three TET family genes, and down-regulation of REST/NRSF. Genes located on chr21 were up-regulated by a median of 45% in DS compared to normal villi, while genes with promoter hypermethylation were down regulated. DNA methylation comparison in human placenta between 6 normal and 11 Trisomy 21 samples

2013-08-06 | E-GEOD-42074 | biostudies-arrayexpress

Global DNA Hypermethylation in Down Syndrome Placenta [RNA-Seq]

Project description:We have performed genome-wide DNA methylation analysis at single base resolution and gene expression analysis, resulted in hypermethylation in all autosomes in DS samples, mediated by down-regulation of all three TET family genes, and down-regulation of REST/NRSF. Genes located on chr21 were up-regulated by a median of 45% in DS compared to normal villi, while genes with promoter hypermethylation were down regulated. Comparison of RNA expression in human placenta between 5 normal and 4 Trisomy 21 samples.

2013-08-06 | E-GEOD-42142 | biostudies-arrayexpress

Global DNA hypermethylation in down syndrome placenta.

Project description: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.

| S-EPMC3675012 | biostudies-literature

Global DNA Hypermethylation in Down Syndrome Placenta

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-08-06 | GSE42144 | GEO

Global DNA Hypermethylation in Down Syndrome Placenta [RNA-Seq]

2013-08-06 | GSE42142 | GEO

Global DNA Hypermethylation in Down Syndrome Placenta [Bisulfite-Seq]

2013-08-06 | GSE42074 | GEO

FBXL10 Protects Polycomb-bound Genes from Hypermethylation

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-04-06 | E-GEOD-65583 | biostudies-arrayexpress

FBXL10 and the Protection of Polycomb-bound Genes from Hypermethylation (RRBS)

Project description:Nearly all CpG-dense promoters are occupied by the multi-domain chromosomal protein FBXL10. We show here that complete inactivation of the Fbxl10 gene leads to dense de novo methylation only of the promoters that are co-occupied by both FBXL10 and by Polycomb Repressive Complexes; this results in pervasive defects in embryonic development and death of homozygous Fbxl10 mutant embryos at midgestation. Deletion of key components of Polycomb Repressive Complexes 1 and 2 did not lead to ectopic de novo methylation. These results indicate that FBXL10 defends Polycomb-occupied promoters against ectopic de novo methylation. FBXL10 is the first reported factor whose loss leads to a gain in genomic DNA methylation. DNA methylation analysis using RRBS and expression analysis using RNA-seq was performed on WT and Fbxl10T/T ES cells.

2015-04-06 | E-GEOD-65580 | biostudies-arrayexpress

Global hypermethylation in fetal cortex of Down syndrome due to DNMT3L overexpression.

Project description:Down syndrome (DS) is caused by a triplication of chromosome 21 (HSA21). Increased oxidative stress, decreased neurogenesis and synaptic dysfunction from HSA21 gene overexpression are thought to cause mental retardation, dementia and seizure in this disorder. Recent epigenetic studies have raised the possibility that DNA methylation has significant effects on DS neurodevelopment. Here, we performed methylome profiling in normal and DS fetal cortices and observed a significant hypermethylation in ∼4% of probes in the DS samples compared with age-matched normals. The probes with differential methylation were distributed across all chromosomes, with no enrichment on HSA21. Functional annotation and pathway analyses showed that genes in the ubiquitination pathway were significantly altered, including: BRCA1, TSPYL5 and PEX10 HSA21 located DNMT3L was overexpressed in DS neuroprogenitors, and this overexpression increased the promoter methylation of TSPYL5 potentially through DNMT3B, and decreased its mRNA expression. DNMT3L overexpression also increased mRNA levels for TP53 and APP, effectors of TSPYL5 Furthermore, DNMT3L overexpression increased APP and PSD95 expression in differentiating neurons, whereas DNMT3LshRNA could partially rescue the APP and PSD95 up-regulation in DS cells. These results provide some of the first mechanistic insights into causes for epigenetic changes in DS, leading to modification of genes relevant for the DS neural endophenotype.

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Domains of genomewide gene expression dysregulation in Down syndrome [RRBS]

Project description:Trisomy 21 (T21) is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in T21, and to eliminate the noise of the genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for T21. Here we show that the differential expression between the twins is organized in domains along all chromosomes that are either up- or downregulated. These gene expression dysregulation domains (GEDDs) can be defined by the expression level of their gene content, and are well conserved in induced pluripotent stem cells derived from the twins’ fibroblasts. Comparison of the transcriptome of the Ts65Dn mouse model of DS and wild-type, also showed GEDDs along the mouse chromosomes that were syntenic in human. The GEDDs correlate with the lamina-associated (LADs) and replication domains of mammalian cells. The overall LADs position was not altered in trisomic cells. However, the H3K4me3 profile of the trisomic fibroblasts was modified and accurately followed the GEDD pattern. These results suggest that the nuclear compartments of trisomic cells undergo modifications of the chromatin environment influencing the overall transcriptome and that GEDDs may therefore contribute to some T21 phenotypes. Reduced representation bisulfite sequencing in monozygotic twins discordant for trisomy 21

2014-04-08 | E-GEOD-55505 | biostudies-arrayexpress

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