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

A. M.Mahedi Hasan; Benura Azeroglu; David R.F. Leach

doi:10.1016/bs.mie.2018.09.001

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

School of Biological Sciences

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Abstract / Description of output

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 language	English
Title of host publication	Methods in Enzymology
Publisher	Elsevier
Chapter	22
Pages	523-554
Number of pages	32
Volume	612
ISBN (Print)	9780128159934
DOIs	https://doi.org/10.1016/bs.mie.2018.09.001
Publication status	Published - 28 Nov 2018

Publication series

Name	Methods in Enzymology
Volume	612
ISSN (Print)	0076-6879
ISSN (Electronic)	1557-7988

Keywords / Materials (for Non-textual outputs)

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

Access to Document

10.1016/bs.mie.2018.09.001

Cite this

@inbook{4c26b8c2d0b54a7d9a1fef6ab606ce8a,

title = "Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli",

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.",

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

author = "Hasan, {A. M.Mahedi} and Benura Azeroglu and Leach, {David R.F.}",

year = "2018",

month = nov,

day = "28",

doi = "10.1016/bs.mie.2018.09.001",

language = "English",

isbn = "9780128159934",

volume = "612",

series = "Methods in Enzymology",

publisher = "Elsevier",

pages = "523--554",

booktitle = "Methods in Enzymology",

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TY - CHAP

T1 - Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli

AU - Hasan, A. M.Mahedi

AU - Azeroglu, Benura

AU - Leach, David R.F.

PY - 2018/11/28

Y1 - 2018/11/28

N2 - 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.

AB - 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.

KW - Chromatin immunoprecipitation

KW - DNA double-strand break repair

KW - DNA replication

KW - Escherichia coli

KW - Homologous recombination

KW - Marker frequency analysis

UR - http://www.scopus.com/inward/record.url?scp=85054629254&partnerID=8YFLogxK

U2 - 10.1016/bs.mie.2018.09.001

DO - 10.1016/bs.mie.2018.09.001

M3 - Chapter

C2 - 30502957

AN - SCOPUS:85054629254

SN - 9780128159934

VL - 612

T3 - Methods in Enzymology

SP - 523

EP - 554

BT - Methods in Enzymology

PB - Elsevier

ER -

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

Abstract / Description of output

Publication series

Keywords / Materials (for Non-textual outputs)

Access to Document

Other files and links

Fingerprint

DNA Misfolding and the Maintenance of Genome Stability: an Integrated Molecular, Cellular and Genomic Investigation of DNA Double-Strand Break Repair

Future-Proofing the sustainability of the MRC high throughput sequencing hub in Scotland

Ark Genomics

Cite this

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

Abstract / Description of output

Publication series

Keywords / Materials (for Non-textual outputs)

Access to Document

Other files and links

Fingerprint

Projects

DNA Misfolding and the Maintenance of Genome Stability: an Integrated Molecular, Cellular and Genomic Investigation of DNA Double-Strand Break Repair

Future-Proofing the sustainability of the MRC high throughput sequencing hub in Scotland

Ark Genomics

Cite this