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DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies

ABSTRACT: DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies

PROVIDER: PRJNA690116 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13372862_1.fastq.gz	Fastqsanger.gz
	SRR13372862_2.fastq.gz	Fastqsanger.gz
	SRR13372863_1.fastq.gz	Fastqsanger.gz
	SRR13372863_2.fastq.gz	Fastqsanger.gz
	SRR13372864_1.fastq.gz	Fastqsanger.gz

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DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies

Project description:Mutations in LMNA, encoding Lamin A/C, lead to a variety of diseases known as laminopathies that include dilated cardiomyopathy (DCM). The role of epigenetic mechanisms. such as DNA methylation, has not been thoroughly investigated. Furthermore, the impact of patient-specific LMNA mutations on DNA methylation is unknown. To explore the role of DNA methylation in the context of unique LMNA mutations, we performed reduced representation bisulfite sequencing (RRBS) on ten pairs of fibroblasts and their induced pluripotent stem cell (iPSC) derivatives from two families with DCM due to distinct LMNA mutations. Family-specific differentially methylated regions (DMRs) were identified by comparing the DNA methylation landscape of patient and control samples. Fibroblast DMRs were found to enrich for distal regulatory features and transcriptionally repressed chromatin and to associate with genes related to phenotypes found in laminopathies. These DMRs, in combination with transcriptome-wide expression data and Lamina-associated domain (LAD) organization, revealed the presence of inter-family epimutation hotspots near differentially expressed genes, most of which were located near redistributed LADs. Comparison of DMRs found in fibroblasts and iPSCs identified regions where epimutations were persistent across both cell types. Finally, a network of disease-associated genes dysregulated in LMNA mutated cells was uncovered, potentially due to aberrant methylation changes. In conclusion, the use of in vitro culture models of patient-derived cells and differential methylation analysis enabled the identification of epimutation hotspots and dysregulated genes, consistent with a Lamin A/C mutation-specific epigenetic disease mechanism that arose in somatic and early-developmental cell stages.

2021-07-20 | GSE164365 | GEO

Molecular properties of epimutation hotspots

Project description:Mistakes in the maintenance of CG methylation is a source of heritable epimutations in plants. Multigenerational surveys indicate that the rate of these stochastic events varies substantially across the genome, with some regions harboring localized “epimutation hotspots”. Using Arabidopsis as a model, we show that epimutation hotspots are indexed by a specific set of chromatin states (CS) that map to sub-regions of gene body methylation genes. Although these regions comprise only ~12% of all CGs in the genome, they account for ~63% of all epimutation events per unit time. Molecular profiling revealed that these regions contain unique sequence features, harbor steady-state intermediate methylation levels, and act as putative targets of antagonistic DNA methylation pathways. We further demonstrate that experimentally-induced shifts in steady-state methylation in these hotspot regions are sufficient to significantly alter local epimutation intensities. Our work thus lays foundation for dissecting the molecular mechanisms of epimutation hotspots in plants.

2021-12-02 | GSE178684 | GEO

Dilated Cardiomyopathy

Project description:Dilated Cardiomyopathy

| PRJNA1006418 | ENA

Molecular properties of epimutation hotspots

Project description:Molecular properties of epimutation hotspots

| PRJNA740019 | ENA

DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies.

Project description:BackgroundMutations in LMNA, encoding lamin A/C, lead to a variety of diseases known as laminopathies including dilated cardiomyopathy (DCM) and skeletal abnormalities. Though previous studies have investigated the dysregulation of gene expression in cells from patients with DCM, the role of epigenetic (gene regulatory) mechanisms, such as DNA methylation, has not been thoroughly investigated. Furthermore, the impact of family-specific LMNA mutations on DNA methylation is unknown. Here, we performed reduced representation bisulfite sequencing on ten pairs of fibroblasts and their induced pluripotent stem cell (iPSC) derivatives from two families with DCM due to distinct LMNA mutations, one of which also induces brachydactyly.ResultsFamily-specific differentially methylated regions (DMRs) were identified by comparing the DNA methylation landscape of patient and control samples. Fibroblast DMRs were found to enrich for distal regulatory features and transcriptionally repressed chromatin and to associate with genes related to phenotypes found in tissues affected by laminopathies. These DMRs, in combination with transcriptome-wide expression data and lamina-associated domain (LAD) organization, revealed the presence of inter-family epimutation hotspots near differentially expressed genes, most of which were located outside LADs redistributed in LMNA-related DCM. Comparison of DMRs found in fibroblasts and iPSCs identified regions where epimutations were persistent across both cell types. Finally, a network of aberrantly methylated disease-associated genes revealed a potential molecular link between pathways involved in bone and heart development.ConclusionsOur results identified both shared and mutation-specific laminopathy epimutation landscapes that were consistent with lamin A/C mutation-mediated epigenetic aberrancies that arose in somatic and early developmental cell stages.

| S-EPMC8272901 | biostudies-literature

Cardiac fibroblasts of dilated cardiomyopathy patients

Project description:Cardiac fibroblasts of dilated cardiomyopathy patients

| PRJNA926632 | ENA

Cardiac fibroblasts of dilated cardiomyopathy patients

Project description:To investigate the physiological characteristics of cardiac fibroblasts (CF) from pediatric dilated cardiomyopathy (DCM) patients, CFs were harvested from left ventricular free wall at the heart transplantation. We then performed RNA-seq for 7 different lines of CFs.

2023-09-12 | GSE223517 | GEO

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Project description:Dilated cardiomyopathy vs Myocarditis

| PRJNA493608 | ENA

RNA-sequencing of pediatric idiopathic dilated cardiomyopathy patients and healthy controls

Project description:We used NGS of rna to understand transcriptome wide changes that occur in the left ventricles of pediatric idiopathic dilated cardiomyopathy patients.

2017-09-05 | GSE99321 | GEO

Dilated Cardiomyopathy in Dobermans and Boxers

Project description:This study attempts at investigating the changes in cardiac gene expression that occur in Dilated Cardiomyopathy (DCM). DCM in Dobermans and Boxers are the focus of this study. Control heart tissue as well as Pacing tissue used is from mongrel dogs. Keywords: control vs pacing vs disease; strain specific disease 3 Dobermans-DCM, 4 Boxers-DCM, 3 mongrels-control and 3 mongrels-pacing

2008-05-08 | E-GEOD-11015 | biostudies-arrayexpress

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