Neuron enriched nuclear proteome isolated from human brain

J Proteome Res. 2013 Jul 5;12(7):3193-206. doi: 10.1021/pr400246t. Epub 2013 Jun 17.


The brain consists of diverse cell types including neurons, astrocytes, oligodendrocytes, and microglia. The isolation of nuclei from these distinct cell populations provides an opportunity to identify cell-type-specific nuclear proteins, histone modifications, and regulation networks that are altered with normal brain aging or neurodegenerative disease. In this study, we used a method by which intact neuronal and non-neuronal nuclei were purified from human post-mortem brain employing a modification of fluorescence activated cell sorting (FACS) termed fluorescence activated nuclei sorting (FANS). An antibody against NeuN, a neuron specific splicing factor, was used to isolate neuronal nuclei. Utilizing mass spectrometry (MS) based label-free quantitative proteomics, we identified 1755 proteins from sorted NeuN-positive and negative nuclear extracts. Approximately 20% of these proteins were significantly enriched or depleted in neuronal versus non-neuronal populations. Immunoblots of primary cultured rat neuron, astrocyte, and oligodendrocyte extracts confirmed that distinct members of the major nucleocytoplasmic structural linkage complex (LINC), nesprin-1 and nesprin-3, were differentially enriched in neurons and astrocytes, respectively. These comparative proteomic data sets also reveal a number of transcription and splicing factors that are selectively enriched in a cell-type-specific manner in human brain.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Astrocytes / metabolism
  • Brain / metabolism*
  • Cell Nucleus / metabolism*
  • Cytoskeletal Proteins
  • Epigenesis, Genetic / genetics
  • Humans
  • Microfilament Proteins / isolation & purification
  • Nerve Tissue Proteins / isolation & purification
  • Neurons / metabolism*
  • Nuclear Proteins / isolation & purification*
  • Proteomics / methods


  • Cytoskeletal Proteins
  • Microfilament Proteins
  • Nerve Tissue Proteins
  • Nuclear Proteins
  • SYNE1 protein, human
  • SYNE3 protein, human