Nucleoid-Associated Proteins: Genome Level Occupancy and Expression Analysis

Methods Mol Biol. 2017;1624:85-97. doi: 10.1007/978-1-4939-7098-8_8.


The advent of Chromatin Immunoprecipitation sequencing (ChIP-Seq) has allowed the identification of genomic regions bound by a DNA binding protein in-vivo on a genome-wide scale. The impact of the DNA binding protein on gene expression can be addressed using transcriptome experiments in appropriate genetic settings. Overlaying the above two sources of data enables us to dissect the direct and indirect effects of a DNA binding protein on gene expression. Application of these techniques to Nucleoid Associated Proteins (NAPs) and Global Transcription Factors (GTFs) has underscored the complex relationship between DNA-protein interactions and gene expression change, highlighting the role of combinatorial control. Here, we demonstrate the usage of ChIP-Seq to infer binding properties and transcriptional effects of NAPs such as Fis and HNS, and the GTF CRP in the model organism Escherichia coli K12 MG1655 (E. coli).

Keywords: ChIP-Seq; GTF; MACS; NAP; Regulation of transcription initiation; Z-score.

MeSH terms

  • Binding Sites
  • Chromatin Immunoprecipitation / methods*
  • Computational Biology
  • Cyclic AMP Receptor Protein / chemistry
  • Cyclic AMP Receptor Protein / metabolism
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism*
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism
  • Factor For Inversion Stimulation Protein / chemistry
  • Factor For Inversion Stimulation Protein / metabolism
  • Gene Expression
  • Gene Expression Profiling / methods*
  • Genome, Bacterial
  • Sequence Analysis, DNA / methods*
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism*


  • Cyclic AMP Receptor Protein
  • DNA, Bacterial
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Factor For Inversion Stimulation Protein
  • Fis protein, E coli
  • Transcription Factors
  • crp protein, E coli
  • hns protein, E coli