Getting Down to Specifics: Profiling Gene Expression and Protein-DNA Interactions in a Cell Type-Specific Manner

Adv Genet. 2015;91:103-151. doi: 10.1016/bs.adgen.2015.06.003. Epub 2015 Jul 23.


The majority of multicellular organisms are comprised of an extraordinary range of cell types, with different properties and gene expression profiles. Understanding what makes each cell type unique and how their individual characteristics are attributed are key questions for both developmental and neurobiologists alike. The brain is an excellent example of the cellular diversity expressed in the majority of eukaryotes. The mouse brain comprises of approximately 75 million neurons varying in morphology, electrophysiology, and preferences for synaptic partners. A powerful process in beginning to pick apart the mechanisms that specify individual characteristics of the cell, as well as their fate, is to profile gene expression patterns, chromatin states, and transcriptional networks in a cell type-specific manner, i.e., only profiling the cells of interest in a particular tissue. Depending on the organism, the questions being investigated, and the material available, certain cell type-specific profiling methods are more suitable than others. This chapter reviews the approaches presently available for selecting and isolating specific cell types and evaluates their key features.

Keywords: BiTS-ChIP; Cell isolation; Cell type-specific profiling; ChIP; FACS; INTACT; MACS; Model organisms; Targeted DamID (TaDa); Transcriptomics.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Cytological Techniques
  • DNA-Binding Proteins / metabolism
  • Gene Regulatory Networks
  • Humans
  • Organ Specificity
  • Transcriptome*


  • DNA-Binding Proteins