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Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli

Research output: Chapter in Book/Report/Conference proceedingChapter

Original languageEnglish
Title of host publicationMethods in Enzymology
PublisherElsevier Inc.
Chapter22
Pages523-554
Number of pages32
Volume612
ISBN (Print)9780128159934
DOIs
Publication statusPublished - 28 Nov 2018

Publication series

NameMethods in Enzymology
Volume612
ISSN (Print)0076-6879
ISSN (Electronic)1557-7988

Abstract

Counting DNA whole genome sequencing reads is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyze the genomic consequences of DSBR. We provide detailed procedures for the preparation of DNA and the analysis of data. We compare different ways of visualizing ChIP data and show that alternative protocols for the preparation of DNA for MFA differentially affect the recovery of branched DNA molecules containing Holliday junctions.

    Research areas

  • Chromatin immunoprecipitation, DNA double-strand break repair, DNA replication, Escherichia coli, Homologous recombination, Marker frequency analysis

ID: 77589004