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

A. M.Mahedi Hasan, Benura Azeroglu, David R.F. Leach*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter


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.

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

Publication series

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


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


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