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

Ana J. Chucair-Elliott, Sarah R. Ocañas, David R. Stanford, Victor A. Ansere, Kyla B. Buettner, Hunter Porter, Nicole L. Eliason, Justin Reid, Amanda L. Sharpe, Michael B. Stout, Michael J. Beckstead, Benjamin F. Miller, Arlan Richardson, View ORCID ProfileWillard M. Freeman
doi: https://doi.org/10.1101/862722
Ana J. Chucair-Elliott
1Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
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Sarah R. Ocañas
1Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
2Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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David R. Stanford
1Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
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Victor A. Ansere
1Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
2Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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Kyla B. Buettner
1Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
2Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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Hunter Porter
1Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
3Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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Nicole L. Eliason
4Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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Justin Reid
5Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City OK USA
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Amanda L. Sharpe
4Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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Michael B. Stout
6Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK USA
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Michael J. Beckstead
5Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City OK USA
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Benjamin F. Miller
5Aging & Metabolism Program, Oklahoma Medical Research Foundation, Oklahoma City OK USA
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Arlan Richardson
7Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
8Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK USA
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Willard M. Freeman
1Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, OK USA
8Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK USA
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  • ORCID record for Willard M. Freeman
  • For correspondence: bill-freeman@omrf.org
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Abstract

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 CNS cell types. Paired analysis of the transcriptome and DNA modifications in astrocytes and microglia demonstrates differential usage of DNA methylation and hydroxymethylation in CG and non-CG 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 CNS cell type for which a cell type-specific cre is available.

Footnotes

  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140271

  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140974

  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140895

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted December 03, 2019.
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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia
Ana J. Chucair-Elliott, Sarah R. Ocañas, David R. Stanford, Victor A. Ansere, Kyla B. Buettner, Hunter Porter, Nicole L. Eliason, Justin Reid, Amanda L. Sharpe, Michael B. Stout, Michael J. Beckstead, Benjamin F. Miller, Arlan Richardson, Willard M. Freeman
bioRxiv 862722; doi: https://doi.org/10.1101/862722
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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia
Ana J. Chucair-Elliott, Sarah R. Ocañas, David R. Stanford, Victor A. Ansere, Kyla B. Buettner, Hunter Porter, Nicole L. Eliason, Justin Reid, Amanda L. Sharpe, Michael B. Stout, Michael J. Beckstead, Benjamin F. Miller, Arlan Richardson, Willard M. Freeman
bioRxiv 862722; doi: https://doi.org/10.1101/862722

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