Identification of Transcription Factor-DNA Interactions In Vivo

Subcell Biochem. 2011;52:175-91. doi: 10.1007/978-90-481-9069-0_8.


Recent technological developments have revolutionized our understanding of transcriptional regulation by providing an unprecedented ability to interrogate in vivo transcription factor binding. The combination of high-throughput sequencing with chromatin precipitation of transcription factors and specifically labeled histones has allowed direct protein-DNA contacts to be visualized across genomes as large and complex as mammals at base-pair resolution. This chapter reviews the developments that led to these insights, with particular focus on examples of early protein-DNA localization experiments using genomic microarrays in mammals and yeast. Four state-of-the-art research directions are highlighted as examples of previously unimaginable frontiers now under active investigation.

MeSH terms

  • Animals
  • Chromatin
  • DNA* / metabolism
  • DNA-Binding Proteins / genetics
  • Histones / metabolism
  • Transcription Factors* / genetics


  • Chromatin
  • DNA-Binding Proteins
  • Histones
  • Transcription Factors
  • DNA