High-resolution characterization of DNA/protein complexes in living bacteria

Nicole A. Becker, Justin P. Peters, L. James Maher

Research output: Chapter in Book/Report/Conference proceedingChapter


The occurrence of DNA looping is ubiquitous. This process plays a well-documented role in the regulation of prokaryotic gene expression, such as the Escherichia coli lactose (lac) operon. Here, we present two complementary methods for high-resolution in vivo detection of DNA/protein binding within the bacterial nucleoid by using either chromatin immunoprecipitation combined with phage λ exonuclease digestion (ChIP-exo) or chromatin endogenous cleavage (ChEC), coupled with ligation-mediated polymerase chain reaction (LM-PCR) and Southern blot analysis. As an example we apply these in vivo protein-mapping methods to E. coli to show direct binding of architectural proteins in the Lac repressor-mediated DNA repression loop.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages21
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Architectural proteins
  • Chromatin endogenous cleavage (ChEC)
  • Chromatin immunoprecipitation (ChIP)
  • High-resolution mapping
  • Lac repression loop
  • Ligation-mediated PCR (LM-PCR)
  • Phage lambda exonuclease
  • Polymerase chain reaction (PCR)
  • Southern blot

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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