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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: LPS Experiment RNA-Seq Data

ABSTRACT: Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: LPS Experiment RNA-Seq Data

PROVIDER: PRJNA591599 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10529525_1.fastq.gz	Fastqsanger.gz
	SRR10529525_2.fastq.gz	Fastqsanger.gz
	SRR10529526_1.fastq.gz	Fastqsanger.gz
	SRR10529526_2.fastq.gz	Fastqsanger.gz
	SRR10529527_1.fastq.gz	Fastqsanger.gz

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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: LPS Experiment RNA-Seq Data

Project description:Studies of neuroepigenetic mechanisms in health and disease are hindered by a lack of approaches to analyze both the transcriptome and epigenome of specific cell types isolated from the complex milieu of the CNS. Cell isolation by cell surface markers is complicated by preparation artifacts, changes in markers with experimental conditions, and lack of specific markers. This study validates a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach with tamoxifen (Tam) inducible cell-type specific cre recombination to allow the parallel interrogation of the epigenome and the transcriptome in astrocytes (Aldh1l1-creERT2) or microglia (Cx3cr1-creERT2). The recombined NuTRAP construct labels, in a cell-type specific manner, nuclei (RanGAP1) with biotin and mCherry, and the ribosomes (L10a) with EGFP, enabling INTACT isolation of DNA and TRAP isolation of RNA. Validation experiments by flow cytometry and imaging demonstrate cell-type specific induction of the NuTRAP construct. Transcriptomic studies demonstrate isolation of highly enriched RNA by TRAP and oxidative bisulfite studies of INTACT-isolated DNA demonstrate differential DNA modification patterns in microglia and astrocytes. LPS administration in Cx3cr1 NuTRAP mice demonstrates that microglia-specific transcriptome and epigenome changes are revealed that cannot be detected with tissue-level samples. These experiments demonstrate that the NuTRAP approach can be applied to CNS cell populations and that INTACT approaches can be used to study DNA modifications. These results also provide an approach for generation and validation of NuTRAP neuroscience models crossed to any relevant cell-type specific cre line.

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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: RNA-Seq Data

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Project description:Epigenetic regulation of gene expression occurs in a cell type-specific manner. Current cell-type specific neuroepigenetic studies rely on cell sorting methods that can alter cell phenotype and introduce potential confounds. Here we demonstrate and validate a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach for temporally controlled labeling and isolation of ribosomes and nuclei, and thus RNA and DNA, from specific central nervous system cell types. Analysis of gene expression and DNA modifications in astrocytes or microglia from the same animal demonstrates differential usage of DNA methylation and hydroxymethylation in CpG and non-CpG contexts that corresponds to cell type-specific gene expression. Application of this approach in LPS treated mice uncovers microglia-specific transcriptome and epigenome changes in inflammatory pathways that cannot be detected with tissue-level analysis. The NuTRAP model and the validation approaches presented can be applied to any brain cell type for which a cell type-specific cre is available.

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