High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria.

Nicole A Becker, Justin P Peters, L James Maher

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Nicole A BeckerDepartment of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.

Justin P PetersDepartment of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.

L James MaherDepartment of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA. maher@mayo.edu.

Funding

Enhancement of Cellular DNA FlexibilityR01GM075965 · NIGMS · MAYO CLINIC ROCHESTER · PI MAHER, LOUIS JAMES · 2006 to 2018

$4.2M

NIGMS NIH HHS R01 GM075965

6 · The paper itself

Abstract

The occurrence of DNA looping is ubiquitous. This process plays a well-documented role in the regulation of prokaryotic gene expression, such as in regulation of 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.

Indexed as

Chromatin ImmunoprecipitationDNA, BacterialEscherichia coliBacteriophage lambdaBlotting, SouthernDNA-Binding ProteinsEscherichia coli ProteinsLac OperonPolymerase Chain ReactionProtein BindingDNA, BacterialDNA-Binding ProteinsEscherichia coli ProteinsArchitectural proteinsChromatin endogenous cleavage (ChEC)Chromatin immunoprecipitation (ChIP)High-resolution mappingLac repression loopLigation-mediated PCR (LM-PCR)Phage lambda exonucleasePolymerase chain reaction (PCR)Southern blot

Identifiers

PMID39028504

DOI10.1007/978-1-0716-3930-6_6

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.