Homologous Recombination, 1st ed. 2021
Methods and Protocols
Methods in Molecular Biology Series, Vol. 2153

This volume explores homologous recombination?s (HR) essential role in meiotic and somatic cells. It discusses the analysis of different steps of the HR process from the genetic, molecular biology, and cell biology perspectives. Using a variety of model systems, chapters in this book cover topics such as the genome-wide mapping of DNA double-strand breaks (DSB); analysis of DNA-end resection and recombination intermediates by gel electrophoresis and southern blotting; cell-based monitoring of HR activity in meiotic and mitotic cells; in vitro analysis of branch migration, DNA strand exchange and Holliday junction resolution; or super resolution imaging of HR repair at collapsed replication forks. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, Homologous Recombination: Methods and Protocols is a valuable resource that uses both classical and more recent approaches to answer questions on the HR mechanism. It is a useful tool for scientists working on the field of genome integrity, as well as those working in cancer biology and DNA repair. 

Preface…
Table of Contents…
Contributing Authors…

1 Detection of DNA Double Strand Breaks by γ-H2AX Immunodetection
Sonia I. Barroso and Andrés Aguilera

2 END-seq: An Unbiased, High-Resolution and Genome-Wide Approach to Map DNA Double Strand Breaks and Resection in Human Cells
Nancy Wong, Sam John, André Nussenzweig, and Andres Canela

3 Resection of a DNA Double-Strand Break by Alkaline Gel Electrophoresis and Southern Blotting
Erika Casari, Elisa Gobbini, Michela Clerici, and Maria Pia Longhese

4 Analysis of DNA Double-Strand Break Ends Resection and Single-Strand Annealing in S. pombe
Zhenxin Yan, Sandeep Kumar, and Grzegorz Ira

5 Quantifying DNA End Resection in Human Cells
Yi Zhou and Tanya T. Paull

6 Genetic and Molecular approaches to Study Chromosomal Breakage at Secondary Structure-Forming Repeats
Anissia Ait Saada, Alex Costa, and Kirill S. Lobachev

7 Biochemical analysis of D-Loop Extension and DNA Strand Displacement Synthesis
Youngho Kwon and Patrick Sung

8 DNA Strand Exchange to Monitor Human RAD51-Mediated Strand Invasion and Pairing
Sudipta Lahiri and Ryan B. Jensen

9 Monitoring Homologous Recombination Activity in Human Cells
Domagoj Vugic, Åsa Ehlén, and Aura Carreira

10 Inter-Homolog Homologous Recombination in Mouse Embryonic Stem Cells
Fabio Vanoli, Rohit Prakash, Travis White, and Maria Jasin

11 Branch Migration Activity of Rad54 Protein
Olga M. Mazina and Alexander V. Mazin

12 Holliday Junction Resolution
Raquel Carreira, F. Javier Aguado, Tomas Lama-Diaz, and Miguel G. Blanco

13 Identification and Analysis of Different Types of UFBs
Simon Gemble and Mounira Amor-Guéret

14 Intrachromosomal Recombination in Yeast
Anastasiya Epshtein, Lorraine S. Symington, and Hannah L. Klein

15 Genome-Wide Analysis of Mitotic Recombination in Budding Yeast
Lydia R. Heasley, Nadia M. V. Sampaio, and Juan Lucas Argüeso

16 Monitoring Gene Conversion in Budding Yeast by Southern Blot Analysis
Miyuki Yamaguchi and James E. Haber

17 DNA Double-Strand Break Induced Gene Amplification in Yeast
Tomas Strucko, Michael Lisby, and Uffe Hasbro Mortensen

18 Measuring Chromosome Pairing during Homologous Recombination in Yeast
Fraulin Joseph, So Jung Lee, Eric Bryant, and Rodney Rothstein

19 Cytological Monitoring of Meiotic Crossovers in Spermatocytes and Oocytes
Yan Yun, Masaru Ito, Sumit Sandhu, and Neil Hunter

20 Detection of DSBs in C. elegans Meiosis
Tatiana García-Muse

21 Methods to Map Meiotic Recombination Proteins in Saccharomyces cerevisiae
Aurore Sanchez and Valérie Borde

22 Investigation of Break-Induced Replication in Yeast
Beth Osia, Rajula Elango, Juraj Kramara, Steven A. Roberts, and Anna Malkova

23 Measurement of Homologous Recombination at Stalled Mammalian Replication Forks
Nicholas A. Willis and Ralph Scully

24 Super Resolution Imaging of Homologous Recombination Repair at Collapsed Replication Forks
Donna R. Whelan and Eli Rothenberg

25 The Analysis of Recombination-Dependent Processing of Blocked Replication Forks by Bi-Dimensional Gel Electrophoresis
Karol Kramarz, Anissia Ait Saada and Sarah A.E. Lambert

26 The Sister Chromatid Exchange Assay in Human Cells
Emanuela Tumini and Andrés Aguilera

27 Analysis of Recombination at Yeast Telomeres
Marie-Noelle Simon, Dmitri Churikov and Vincent Géli

28 Gel Electrophoresis Analysis of rDNA Instability in Saccharomyces cerevisiae
Mariko Sasaki and Takehiko Kobayashi

29 Analyzing Homologous Recombination at a Genome Wide Level
Coline Arnould, Vincent Rocher, and Gaëlle Legube

30 CRISPR/Cas9 Induced Breaks in Heterochromatin, Visualized by Immunofluorescence
Mitrentsi Ioanna and Evi Soutoglou

31 In Vivo Binding of Recombination Proteins of Non-DSB DNA Lesions to Replication Forks
Román González-Prieto, María J. Cabello-Lobato and Félix Prado

32 Live Cell Imaging of Nuclear Actin Filaments and Heterochromatic Repair foci in Drosophila and Mouse Cells
Colby See, Deepak Arya, Emily Lin, and Irene Chiolo

33 In Vitro Characterization of Sumoylation of HR Proteins
Veronika Altmannova and Lumir Krejci

34 High-Throughput Analysis of Heteroduplex DNA in Mitotic Recombination Products
Dionna Gamble, Yee Fang Hum, and Sue Jinks-Robertson

35 Fluorescence Microscopy for Analysis of Relocalization of Structure-Specific Endonucleases
Carl P. Lehmann, Irene Saugar, and José Antonio Tercero

36 Physical and Genetic Assays for the Study of DNA Joint Molecules Metabolism and Multi-Invasion-Induced Rearrangements in S. cerevisiae
Aurèle Piazza, Pallavi Rajput, and Wolf-Dietrich Heyer

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts