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Differential usage of DNA modifications in neurons, astrocytes and microglia

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

ORGANISM(S): Mus musculus

PROVIDER: GSE228045 | GEO | 2023/09/22

REPOSITORIES: GEO

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Differential usage of DNA modifications in neurons, astrocytes and microglia [WGoxBS]

Project description:Cellular identity is determined, in part, by cell type-specific epigenomic profiles that govern gene expression. Isolation and epigenomic characterization of specific cell types is greatly needed in neuroscience. While single cell DNA modification studies offer promise to answer this question, these approaches suffer from limited genomic coverage and cannot differentiate between methylation and hydroxymethylation. Thus, approaches to isolate and analyze DNA from specific CNS cell populations are needed. Here we validate a temporally controlled in vivo nuclear tagging mouse model (NuTRAP) and isolation (INTACT) of neuronal nucleic acids. Analysis of differential DNA modifications (methylation and hydroxymethylation) and gene expression in neurons, astrocytes, and microglia demonstrates a common regulatory function for DNA modifications that transcends cell type. Insight into the normal function of DNA modifications in genomic regulation is crucial in order to better understand the epigenomic mechanisms underlying disease.

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Differential usage of DNA modifications in neurons, astrocytes and microglia [RNA-seq]

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Differential responses of neurons, astrocytes, and microglia to G-quadruplex stabilization.

Project description:The G-quadruplex (G4-DNA or G4) is a secondary DNA structure formed by DNA sequences containing multiple runs of guanines. While it is now firmly established that stabilized G4s lead to enhanced genomic instability in cancer cells, whether and how G4s contribute to genomic instability in brain cells is still not clear. We previously showed that, in cultured primary neurons, small-molecule G4 stabilizers promote formation of DNA double-strand breaks (DSBs) and downregulate the Brca1 gene. Here, we determined if G4-dependent Brca1 downregulation is unique to neurons or if the effects in neurons also occur in astrocytes and microglia. We show that primary neurons, astrocytes and microglia basally exhibit different G4 landscapes. Stabilizing G4-DNA with the G4 ligand pyridostatin (PDS) differentially modifies chromatin structure in these cell types. Intriguingly, PDS promotes DNA DSBs in neurons, astrocytes and microglial cells, but fails to downregulate Brca1 in astrocytes and microglia, indicating differences in DNA damage and repair pathways between brain cell types. Taken together, our findings suggest that stabilized G4-DNA contribute to genomic instability in the brain and may represent a novel senescence pathway in brain aging.

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