Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia

Commun Biol. 2020 Nov 19;3(1):693. doi: 10.1038/s42003-020-01418-x.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aldehyde Dehydrogenase 1 Family / genetics
  • Aldehyde Dehydrogenase 1 Family / metabolism
  • Animals
  • Astrocytes / drug effects
  • Astrocytes / metabolism*
  • Cells, Cultured
  • Epigenesis, Genetic*
  • Female
  • Gene Expression Regulation
  • Genetic Markers
  • Lipopolysaccharides / toxicity
  • Male
  • Mice
  • Microglia / drug effects
  • Microglia / metabolism*
  • RNA-Seq
  • Retinal Dehydrogenase / genetics
  • Retinal Dehydrogenase / metabolism
  • Transcriptome*


  • Genetic Markers
  • Lipopolysaccharides
  • Aldehyde Dehydrogenase 1 Family
  • ALDH1A1 protein, mouse
  • Retinal Dehydrogenase

Associated data

  • figshare/10.6084/m9.figshare.12670895
  • figshare/10.6084/m9.figshare.12669698