GSE159106
Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Cx3cr1+;NT+ Hippocampus RNA-Seq Data
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. Overall design: Hippocampi isolated from Cx3cr1-cre/Ert2+; NuTRAP+ mice; RNA isolated via TRAP methods- Input and Positive fractions were sequenced; 3 biological replicates