A simple method for gene expression and chromatin profiling of individual cell types within a tissue

Dev Cell. 2010 Jun 15;18(6):1030-40. doi: 10.1016/j.devcel.2010.05.013.


Understanding the production and function of specialized cells during development requires the isolation of individual cell types for analysis, but this is currently a major technical challenge. Here we describe a method for cell type-specific RNA and chromatin profiling that circumvents many of the limitations of current methods for cell isolation. We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure gene expression and chromatin features of the hair and non-hair cell types of the Arabidopsis root epidermis. We identified hundreds of genes that are preferentially expressed in each cell type and show that genes with the largest expression differences between hair and non-hair cells also show differences between cell types in the trimethylation of histone H3 at lysines 4 and 27. This method should be applicable to any organism that is amenable to transformation.

Publication types

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

MeSH terms

  • Arabidopsis / growth & development*
  • Arabidopsis Proteins / genetics
  • Biotin / chemistry
  • Cell Differentiation / genetics
  • Chromatin / genetics
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Developmental / genetics
  • Gene Expression Regulation, Plant / physiology*
  • Histones / genetics
  • Histones / metabolism
  • Lysine / metabolism
  • Methylation
  • Models, Genetic
  • Molecular Biology / methods*
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Plant Epidermis / growth & development*
  • Plant Roots / growth & development*
  • RNA / genetics
  • Staining and Labeling / methods


  • Arabidopsis Proteins
  • Chromatin
  • Histones
  • Nuclear Proteins
  • RNA
  • Biotin
  • Lysine

Associated data

  • GEO/GSE19654