Chapter title |
High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria
|
---|---|
Chapter number | 6 |
Book title |
Bacterial Chromatin
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-8675-0_6 |
Pubmed ID | |
Book ISBNs |
978-1-4939-8674-3, 978-1-4939-8675-0
|
Authors |
Becker, Nicole A, Peters, Justin P, Maher, L James, Nicole A. Becker, Justin P. Peters, L. James Maher, Becker, Nicole A., Peters, Justin P., Maher, L. James |
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. |
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