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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Acknowledgments
This work was supported by the Mayo Foundation and by National Institutes of Health grant GM75965 to LJM.
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Becker, N.A., Peters, J.P., Maher, L.J. (2018). High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria. In: Dame, R. (eds) Bacterial Chromatin. Methods in Molecular Biology, vol 1837. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8675-0_6
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DOI: https://doi.org/10.1007/978-1-4939-8675-0_6
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