Nuclear RNA-seq of single neurons reveals molecular signatures of activation

Nat Commun. 2016 Apr 19;7:11022. doi: 10.1038/ncomms11022.

Abstract

Single-cell sequencing methods have emerged as powerful tools for identification of heterogeneous cell types within defined brain regions. Application of single-cell techniques to study the transcriptome of activated neurons can offer insight into molecular dynamics associated with differential neuronal responses to a given experience. Through evaluation of common whole-cell and single-nuclei RNA-sequencing (snRNA-seq) methods, here we show that snRNA-seq faithfully recapitulates transcriptional patterns associated with experience-driven induction of activity, including immediate early genes (IEGs) such as Fos, Arc and Egr1. SnRNA-seq of mouse dentate granule cells reveals large-scale changes in the activated neuronal transcriptome after brief novel environment exposure, including induction of MAPK pathway genes. In addition, we observe a continuum of activation states, revealing a pseudotemporal pattern of activation from gene expression alone. In summary, snRNA-seq of activated neurons enables the examination of gene expression beyond IEGs, allowing for novel insights into neuronal activation patterns in vivo.

Publication types

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

MeSH terms

  • Animals
  • Cell Nucleus / genetics
  • Cytoskeletal Proteins / genetics
  • Cytoskeletal Proteins / metabolism
  • Dentate Gyrus / cytology
  • Dentate Gyrus / metabolism
  • Early Growth Response Protein 1 / genetics
  • Early Growth Response Protein 1 / metabolism
  • Gene Ontology
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism
  • Immediate-Early Proteins / genetics
  • Immediate-Early Proteins / metabolism
  • Immunohistochemistry
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Microscopy, Confocal
  • Nerve Tissue Proteins / genetics
  • Nerve Tissue Proteins / metabolism
  • Neurons / metabolism*
  • Proto-Oncogene Proteins c-fos / genetics
  • Proto-Oncogene Proteins c-fos / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods*
  • Transcriptome*
  • Tumor Suppressor Proteins / genetics
  • Tumor Suppressor Proteins / metabolism

Substances

  • Cytoskeletal Proteins
  • Early Growth Response Protein 1
  • Homeodomain Proteins
  • Immediate-Early Proteins
  • Nerve Tissue Proteins
  • Proto-Oncogene Proteins c-fos
  • Tumor Suppressor Proteins
  • activity regulated cytoskeletal-associated protein
  • prospero-related homeobox 1 protein

Associated data

  • GEO/GSE77067