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Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE301387 | GEO | 2025/07/14

REPOSITORIES: GEO

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Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [methylation]

Project description:Overgrowth with Intellectual Disability (OGID) is characterized by generalized overgrowth, including a head circumference and/or height ≥ 2 standard deviations (s.d.) above the mean, accompanied by mild to moderate intellectual disability. Sotos Syndrome, the most common form of OGID, results from loss-of-function (LoF) mutations in NSD1, which encodes a histone methyltransferase. Another major OGID subtype, Tatton-Brown-Rahman syndrome, is caused by LoF mutations in DNMT3A, encoding a de novo DNA methyltransferase. In contrast, gain-of-function (GoF) mutations in DNMT3A cause Heyn-Sproul-Jackson syndrome, characterized by growth restriction and microcephaly. We hypothesize that NSD1 LoF and DNMT3A LoF mutations share a convergent DNA methylation signature that is distinct from the pattern seen in DNMT3A GoF mutations. To test this, we generated human embryonic stem cell lines carrying these growth syndrome-associated mutations in NSD1 and DNMT3A, profiled their DNA methylation patterns using the Illumina EPIC array, and analyzed both shared and unique methylation phenotypes.

2025-07-14 | GSE299394 | GEO

Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [CUT&RUN]

2025-07-14 | GSE301386 | GEO

Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [RNA-seq]

2025-09-27 | GSE309381 | GEO

Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders

Project description:Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders

| PRJNA1284900 | ENA

Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [methylation]

Project description:Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [methylation]

| PRJNA1274349 | ENA

Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [CUT&RUN]

Project description:Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [CUT&RUN]

| PRJNA1284906 | ENA

Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [RNA-seq]

Project description:Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [RNA-seq]

| PRJNA1335282 | ENA

A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice.

Project description:DNA methyltransferases (DNMTs) deposit DNA methylation, which regulates gene expression and is essential for mammalian development. Histone post-translational modifications modulate the recruitment and activity of DNMTs. The PWWP domains of DNMT3A and DNMT3B are posited to interact with histone 3 lysine 36 trimethylation (H3K36me3); however, the functionality of this interaction for DNMT3A remains untested in vivo. Here we present a mouse model carrying a D329A point mutation in the DNMT3A PWWP domain. The mutation causes dominant postnatal growth retardation. At the molecular level, it results in progressive DNA hypermethylation across domains marked by H3K27me3 and bivalent chromatin, and de-repression of developmental regulatory genes in adult hypothalamus. Evaluation of non-CpG methylation, a marker of de novo methylation, further demonstrates the altered recruitment and activity of DNMT3AD329A at bivalent domains. This work provides key molecular insights into the function of the DNMT3A-PWWP domain and role of DNMT3A in regulating postnatal growth.

| S-EPMC6478690 | biostudies-literature

Sperm DNA methylation altered by THC and nicotine: Vulnerability of neurodevelopmental genes with bivalent chromatin.

Project description:Men consume the most nicotine and cannabis products but impacts on sperm epigenetics are poorly characterized. Evidence suggests that preconception exposure to these drugs alters offspring neurodevelopment. Epigenetics may in part facilitate heritability. We therefore compared effects of exposure to tetrahydrocannabinol (THC) and nicotine on DNA methylation in rat sperm at genes involved in neurodevelopment. Reduced representation bisulfite sequencing data from sperm of rats exposed to THC via oral gavage showed that seven neurodevelopmentally active genes were significantly differentially methylated versus controls. Pyrosequencing data revealed majority overlap in differential methylation in sperm from rats exposed to THC via injection as well as those exposed to nicotine. Neurodevelopmental genes including autism candidates are vulnerable to environmental exposures and common features may mediate this vulnerability. We discovered that autism candidate genes are significantly enriched for bivalent chromatin structure, suggesting this configuration may increase vulnerability of genes in sperm to disrupted methylation.

| S-EPMC7525661 | biostudies-literature

A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and postnatal growth retardation in mice

Project description:DNA methyltransferases (DNMTs) deposit repressive DNA methylation, which regulates gene expression and is essential for mammalian development. Histone post-translational modifications can recruit DNMTs to DNA. The PWWP domains of DNMT3A and DNMT3B are posited to interact with histone 3 lysine 36 trimethylation (H3K36me3); however, the functionality of this interaction for DNMT3A remains untested in vivo. Here we present a mouse model carrying a D329A point mutation in the DNMT3A PWWP domain. The mutation causes dominant postnatal growth retardation. At the molecular level, it results in aberrant progressive acquisition of DNA methylation across domains marked by bivalent chromatin, resulting in de-repression of important developmental regulatory genes in adult hypothalamus. Evaluation of non-CpG methylation further demonstrates the altered recruitment and activity of mutant DNMT3A at bivalent domains. This work provides key molecular insights into analogous growth phenotypes observed in humans with congenital mutations in the DNMT3A PWWP domain.

2019-03-18 | GSE117728 | GEO

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