Genome-Wide Identification of Transcription Factor-Binding Sites in Quiescent Adult Neural Stem Cells

Methods Mol Biol. 2018:1686:265-286. doi: 10.1007/978-1-4939-7371-2_19.


Transcription factors bind to specific DNA sequences and control the transcription rate of nearby genes in the genome. This activation or repression of gene expression is further potentiated by epigenetic modifications of histones with active and silent marks, respectively. Resident adult stem cells in the hematopoietic system, skin, and brain exist in a non-proliferative quiescent resting state. When quiescent stem cells become activated and transition to dividing progenitors and distinct cell types, they can replenish and repair tissue. Thus, determination of the position of transcription factor binding and histone epigenetic modification on the chromatin is an essential step toward understanding the gene regulation of quiescent and proliferative adult stem cells for potential applications in regenerative medicine. Genome-wide transcription factor occupancy and histone modifications on the genome can be obtained by assessing DNA-protein interaction through next-generation chromatin immunoprecipitation sequencing technology (ChIP-seq). This chapter outlines the protocol to perform, analyze, and validate ChIP-seq experiments that can be used to identify protein-DNA interactions and histone marks on the chromatin. The methods described here are applicable to quiescent and proliferative neural stem cells, and a wide range of other cellular systems.

Keywords: Bioinformatics; ChIP-qPCR; ChIP-seq; Chromatin sonication; DNA-protein crosslinking; Genome-wide histone modification; Transcription factor genome-wide DNA occupancy.

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

  • Adult
  • Adult Stem Cells / cytology
  • Adult Stem Cells / metabolism*
  • Binding Sites
  • Cells, Cultured
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Chromatin Immunoprecipitation / methods*
  • Epigenesis, Genetic
  • Genome, Human*
  • High-Throughput Nucleotide Sequencing / methods
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Neural Stem Cells / cytology
  • Neural Stem Cells / metabolism*
  • Protein Binding
  • Resting Phase, Cell Cycle*
  • Sequence Analysis, DNA / methods
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*


  • Chromatin
  • Histones
  • Transcription Factors