Homologous Recombination: Methods and Protocols

Front Matter ....Pages i-xv
 Detection of DNA Double-Strand Breaks by γ-H2AX Immunodetection  (Sonia I. Barroso, Andrés Aguilera)....Pages 1-8
 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, Andrés Canela)....Pages 9-31
 Resection of a DNA Double-Strand Break by Alkaline Gel Electrophoresis and Southern Blotting  (Erika Casari, Elisa Gobbini, Michela Clerici, Maria Pia Longhese)....Pages 33-45
 Analysis of DNA Double-Strand Break End Resection and Single-Strand Annealing in S. pombe  (Zhenxin Yan, Sandeep Kumar, Grzegorz Ira)....Pages 47-57
 Quantifying DNA End Resection in Human Cells  (Yi Zhou, Tanya T. Paull)....Pages 59-69
 Genetic and Molecular Approaches to Study Chromosomal Breakage at Secondary Structure–Forming Repeats  (Anissia Ait Saada, Alex B. Costa, Kirill S. Lobachev)....Pages 71-86
 Biochemical Analysis of D-Loop Extension and DNA Strand Displacement Synthesis  (Youngho Kwon, Patrick Sung)....Pages 87-99
 DNA Strand Exchange to Monitor Human RAD51-Mediated Strand Invasion and Pairing  (Sudipta Lahiri, Ryan B. Jensen)....Pages 101-113
 Monitoring Homologous Recombination Activity in Human Cells  (Domagoj Vugic, Åsa Ehlén, Aura Carreira)....Pages 115-126
 Interhomolog Homologous Recombination in Mouse Embryonic Stem Cells  (Fabio Vanoli, Rohit Prakash, Travis White, Maria Jasin)....Pages 127-143
 Branch Migration Activity of Rad54 Protein  (Olga M. Mazina, Alexander V. Mazin)....Pages 145-167
 Holliday Junction Resolution  (Raquel Carreira, F. Javier Aguado, Tomas Lama-Diaz, Miguel G. Blanco)....Pages 169-185
 Identification and Analysis of Different Types of UFBs  (Simon Gemble, Mounira Amor-Guéret)....Pages 187-192
 Intrachromosomal Recombination in Yeast  (Anastasiya Epshtein, Lorraine S. Symington, Hannah L. Klein)....Pages 193-200
 Genome-Wide Analysis of Mitotic Recombination in Budding Yeast  (Lydia R. Heasley, Nadia M. V. Sampaio, Juan Lucas Argueso)....Pages 201-219
 Monitoring Gene Conversion in Budding Yeast by Southern Blot Analysis  (Miyuki Yamaguchi, James E. Haber)....Pages 221-238
 DNA Double-Strand Break-Induced Gene Amplification in Yeast  (Tomas Strucko, Michael Lisby, Uffe Hasbro Mortensen)....Pages 239-252
 Measuring Chromosome Pairing During Homologous Recombination in Yeast  (Fraulin Joseph, So Jung Lee, Eric Edward Bryant, Rodney Rothstein)....Pages 253-265
 Cytological Monitoring of Meiotic Crossovers in Spermatocytes and Oocytes  (Yan Yun, Masaru Ito, Sumit Sandhu, Neil Hunter)....Pages 267-286
 Detection of DSBs in C. elegans Meiosis  (Tatiana García-Muse)....Pages 287-293
 Methods to Map Meiotic Recombination Proteins in Saccharomyces cerevisiae  (Aurore Sanchez, Valérie Borde)....Pages 295-306
 Investigation of Break-Induced Replication in Yeast  (Beth Osia, Rajula Elango, Juraj Kramara, Steven A. Roberts, Anna Malkova)....Pages 307-328
 Measurement of Homologous Recombination at Stalled Mammalian Replication Forks  (Nicholas A. Willis, Ralph Scully)....Pages 329-353
 Super-Resolution Imaging of Homologous Recombination Repair at Collapsed Replication Forks  (Donna R. Whelan, Eli Rothenberg)....Pages 355-363
 The Analysis of Recombination-Dependent Processing of Blocked Replication Forks by Bidimensional Gel Electrophoresis  (Karol Kramarz, Anissia Ait Saada, Sarah A. E. Lambert)....Pages 365-381
 The Sister-Chromatid Exchange Assay in Human Cells  (Emanuela Tumini, Andrés Aguilera)....Pages 383-393
 Analysis of Recombination at Yeast Telomeres  (Marie-Noelle Simon, Dmitri Churikov, Vincent Géli)....Pages 395-402
 Gel Electrophoresis Analysis of rDNA Instability in Saccharomyces cerevisiae  (Mariko Sasaki, Takehiko Kobayashi)....Pages 403-425
 Analyzing Homologous Recombination at a Genome-Wide Level  (Coline Arnould, Vincent Rocher, Gaëlle Legube)....Pages 427-438
 CRISPR/Cas9-Induced Breaks in Heterochromatin, Visualized by Immunofluorescence  (Ioanna Mitrentsi, Evi Soutoglou)....Pages 439-445
 In Vivo Binding of Recombination Proteins to Non-DSB DNA Lesions and to Replication Forks  (Román González-Prieto, María J. Cabello-Lobato, Félix Prado)....Pages 447-458
 Live Cell Imaging of Nuclear Actin Filaments and Heterochromatic Repair foci in Drosophila and Mouse Cells  (Colby See, Deepak Arya, Emily Lin, Irene Chiolo)....Pages 459-482
 In Vitro Characterization of Sumoylation of HR Proteins  (Veronika Altmannova, Lumir Krejci)....Pages 483-502
 High-Throughput Analysis of Heteroduplex DNA in Mitotic Recombination Products  (Dionna Gamble, Yee Fang Hum, Sue Jinks-Robertson)....Pages 503-519
 Fluorescence Microscopy for Analysis of Relocalization of Structure-Specific Endonucleases  (Carl P. Lehmann, Irene Saugar, José Antonio Tercero)....Pages 521-534
 Physical and Genetic Assays for the Study of DNA Joint Molecules Metabolism and Multi-invasion-Induced Rearrangements in S. cerevisiae  (Aurèle Piazza, Pallavi Rajput, Wolf-Dietrich Heyer)....Pages 535-554
Back Matter ....Pages 555-557