Rapid Molecular Profiling of Defined Cell Types Using Viral TRAP

Cell Rep. 2017 Apr 18;19(3):655-667. doi: 10.1016/j.celrep.2017.03.048.


Translational profiling methodologies enable the systematic characterization of cell types in complex tissues, such as the mammalian brain, where neuronal isolation is exceptionally difficult. Here, we report a versatile strategy for profiling CNS cell types in a spatiotemporally restricted fashion by engineering a Cre-dependent adeno-associated virus expressing an EGFP-tagged ribosomal protein (AAV-FLEX-EGFPL10a) to access translating mRNAs by translating ribosome affinity purification (TRAP). We demonstrate the utility of this AAV to target a variety of genetically and anatomically defined neural populations expressing Cre recombinase and illustrate the ability of this viral TRAP (vTRAP) approach to recapitulate the molecular profiles obtained by bacTRAP in corticothalamic neurons across multiple serotypes. Furthermore, spatially restricting adeno-associated virus (AAV) injections enabled the elucidation of regional differences in gene expression within this cell type. Altogether, these results establish the broad applicability of the vTRAP strategy for the molecular dissection of any CNS or peripheral cell type that can be engineered to express Cre.

Keywords: AAV; MCH; Ntsr1; RNA-seq; TRAP; corticothalamic; molecular profiling.

Publication types

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

MeSH terms

  • Animals
  • Biomarkers / metabolism
  • Chromatography, Affinity / methods*
  • Dependovirus / metabolism
  • Female
  • Gene Expression Regulation
  • Green Fluorescent Proteins / metabolism
  • Hypothalamic Hormones / metabolism
  • Hypothalamus / metabolism
  • Male
  • Melanins / metabolism
  • Mice
  • Neurons / metabolism
  • Pituitary Hormones / metabolism
  • Protein Biosynthesis*
  • Reproducibility of Results
  • Ribosomes / metabolism*
  • Serotyping
  • Viruses / metabolism*


  • Biomarkers
  • Hypothalamic Hormones
  • Melanins
  • Pituitary Hormones
  • enhanced green fluorescent protein
  • Green Fluorescent Proteins
  • melanin-concentrating hormone