Characterizing the Epigenomic Heat Shock Response in E. coli with ChIP-exo

Open Access
John, Jordan Denny
Area of Honors:
Bachelor of Science
Document Type:
Thesis Supervisors:
  • Benjamin Franklin Pugh, Thesis Supervisor
  • Michael Axtell, Honors Advisor
  • E. coli
  • ChIP-exo
  • Epigenome
  • Sigma Factors
  • Heat Shock
  • Transcription Factors
Despite E. coli being a model organism for understanding the epigenome of prokaryotes, transcriptional regulation in E. coli is not fully understood. This study aims to provide insight into the genomic occupancies of various RNA polymerase subunits, sigma factors, sequence-specific transcription factors, and nucleoid-associated proteins under normal growth conditions as well as upon acute heat shock. This was done using the ChIP-exo assay that provides near basepair resolution of protein binding on DNA. We show high-resolution binding patterns of the nucleoid-associated proteins, Fis and IHF-beta; sigma factors, sigma 70 and sigma 54; and transcription factor, Crp at their respective motifs. By comparing the DNA shape features at binding sites with high occupancy with those with low occupancy, we found that proteins rely on sequence-specific as well as indirect shape features of DNA to recognize their binding sites. In addition, we observed strong enrichment of the housekeeping sigma factor sigma 70 at the promoters of the genes genome-wide which correlated well with the binding of various polymerase subunits as well as transcription. The occupancies of the nucleoid-associated proteins studied do not correlate well with the sigma factor sigma 70, suggesting that they influence transcription through indirect ways. Additionally, while we did not observe widespread changes in the binding patterns in many proteins upon acute heat shock, we saw upregulation of heat shock responsive sigma factor sigma 32 binding at select genes.