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Faculty Publications
High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria
Document Type
Article
Keywords
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
Journal/Book/Conference Title
Methods in Molecular Biology
Volume
1837
First Page
95
Last Page
115
Abstract
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.
Department
Department of Chemistry and Biochemistry
Original Publication Date
1-1-2018
DOI of published version
10.1007/978-1-4939-8675-0_6
Recommended Citation
Peters, Justin P.; Becker, Nicole A.; and Maher, L. James, "High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria" (2018). Faculty Publications. 6236.
https://scholarworks.uni.edu/facpub/6236