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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (5hmC) [5hmC-Seal]

ABSTRACT: We report the 5hmC in human hippocampus subject to normal aging and Alzheimer's disease.

ORGANISM(S): Homo sapiens

PROVIDER: GSE159671 | GEO | 2020/10/21

REPOSITORIES: GEO

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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (RNA-seq) [RNA-seq]

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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (H3K9ac, H3K27ac, H3K122ac, H3K4me1) [ChIP-Seq]

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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (5hmC) [5hmC-Seal]

Project description:An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (5hmC) [5hmC-Seal]

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Loss of TET3-mediated 5hmC promotes the Neurodegeneration of Alzheimer’s disease

Project description:Alzheimer's disease (AD) was attributed to alterations in multiple epigenetic systems including DNA methylation and demethylation patterns. DNA 5-hydroxymethylcytosin (5hmC), an epigenetic hallmark, plays importantly regulatory role in many biological processes. However, the 5hmC-mediated epigenetic underpinnings of AD neurodegeneration remain poorly understood. Here we report that selective loss of 5hmC is substantially presented in human AD and 3xTg-AD mouse neocortical and hippocampal neurons. Quantitative genome-wide analysis of hMeDIP-seq reveals that neuron-specific shift in decreased 5hmC enrichment in regions of promoter, intergenic and gene body of mRNA and lncRNA genes was found in3xTg-AD mice. We further identified that TET3, an enzyme that converts 5-methylcytosine (5mC) to 5hmC, responded to Beta amyloid neuronal toxicity and was mainly responsible for loss of 5hmC in AD brain. Overexpression of human TET3 catalytic domain (hTET3CD) significantly improves the neuroinflammation, neuropathological progression and cognitive deficits in 3xTg-AD mice. These findings implicate as a potential hallmark, TET3-mediated 5hmC epigenetic dysregulation is involved in driving AD neurodegeneration.

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RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development [5hmC-Seal]

Project description:RNA-seq, WGBS, 5hmC-Seal, and ATAC-seq data about TET proteins and skeletal development [5hmC-Seal]

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Intestinal stem cell differentiation is associated with dynamic changes in the chromatin landscape [5hmc-seal-seq]

Project description:The global localization of 5-hydroxymethylcytosine (5hmc) were measured by 5hmc-seal-seq in four populations of intestinal epithelium defined by their levels of a GFP reporter transgene that is driven by the regulatory elements of the Sox9 gene.

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Maternal Zika virus infection alters epigenetic DNA modifications and leads to transgenerational behavioral changes in offspring mice (5hmC)

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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

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

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5-hydroxymethylcytosine (5hmC) methylation profiling of adult mouse brain and liver tissues (hMeDIP-seq)

Project description:5-hydroxymethylcytosine (5hmC) is the first oxidative product of the TET-mediated 5-methylcytosine (5mC) demethylation pathway. It is a key intermediate in cytosine demethylation, and have potential regulatory functions with emerging importance in mammalian biology. In this work, we used a chemical capture-based technique that coupled with next-generation sequencing to investigate the global 5hmC methylation in five brain subregions (cerebellum, cortex, hippocampus, hypothalamus and thalamus) and liver tissues from female and male adult mice. We also performed total RNA sequencing to study the association between 5hmC and gene expression. The enriched 5-hmC library was sequenced on a HiSeq2500 by paired-end sequencing with 100 bp read length.

2017-01-31 | E-MTAB-5167 | biostudies-arrayexpress

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