Genome Instability: Methods and Protocols

Description

This volume presents forty-two methods and protocols to analyze diverse aspects of genome instability. Chapters detail mutagenesis and repair, methods to quantify and analyze the properties of DNA double-strand breaks, profile replication, replication proteins strand-specifically, genome instability, fluorescence microscopic techniques, and genomic and proteomic approaches. 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. Authoritative and cutting-edge, Genome Instability: Methods and Protocols aims to provide a comprehensive resource for the discovery and analysis of the proteins and pathways that are critical for stable maintenance of the genome. Front Matter ....Pages i-xvi The A-Like Faker Assay for Measuring Yeast Chromosome III Stability (Carolina A. Novoa, J. Sidney Ang, Peter C. Stirling)....Pages 1-9 The Chromosome Transmission Fidelity Assay for Measuring Chromosome Loss in Yeast (Supipi Duffy, Philip Hieter)....Pages 11-19 Measuring Mutation Rates Using the Luria-Delbrück Fluctuation Assay (Gregory I. Lang)....Pages 21-31 Molecular Genetic Characterization of Mutagenesis Using a Highly Sensitive Single-Stranded DNA Reporter System in Budding Yeast (Kin Chan)....Pages 33-42 Analyzing Genome Rearrangements in Saccharomyces cerevisiae (Anjana Srivatsan, Christopher D. Putnam, Richard D. Kolodner)....Pages 43-61 High-Resolution Mapping of Modified DNA Nucleobases Using Excision Repair Enzymes (Monica Ransom, D. Suzi Bryan, Jay R. Hesselberth)....Pages 63-76 Integrated Microarray-based Tools for Detection of Genomic DNA Damage and Repair Mechanisms (Patrick van Eijk, Yumin Teng, Mark R. Bennet, Katie E. Evans, James R. Powell, Richard M. Webster et al.)....Pages 77-99 Study of UV-induced DNA Repair Factor Recruitment: Kinetics and Dynamics (Sarah Sertic, Stefania Roma, Paolo Plevani, Federico Lazzaro, Marco Muzi-Falconi)....Pages 101-105 Inserting Site-Specific DNA Lesions into Whole Genomes (Vincent Pagès, Robert P. Fuchs)....Pages 107-118 A qPCR-Based Protocol to Quantify DSB Resection (Matteo Ferrari, Shyam Twayana, Federica Marini, Achille Pellicioli)....Pages 119-129 Alkaline Denaturing Southern Blot Analysis to Monitor Double-Strand Break Processing (Chiara Vittoria Colombo, Luca Menin, Michela Clerici)....Pages 131-145 Single Molecule Analysis of Resection Tracks (Pablo Huertas, Andrés Cruz-García)....Pages 147-154 Mapping DNA Breaks by Next-Generation Sequencing (Laura Baranello, Fedor Kouzine, Damian Wojtowicz, Kairong Cui, Keji Zhao, Teresa M. Przytycka et al.)....Pages 155-166 Genome-Wide Profiling of DNA Double-Strand Breaks by the BLESS and BLISS Methods (Reza Mirzazadeh, Tomasz Kallas, Magda Bienko, Nicola Crosetto)....Pages 167-194 DNA Replication Profiling Using Deep Sequencing (Xanita Saayman, Cristina Ramos-Pérez, Grant W. Brown)....Pages 195-207 Quantitative Bromodeoxyuridine Immunoprecipitation Analyzed by High-Throughput Sequencing (qBrdU-Seq or QBU) (Joanna E. Haye-Bertolozzi, Oscar M. Aparicio)....Pages 209-225 Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast (Chuanhe Yu, Haiyun Gan, Zhiguo Zhang)....Pages 227-238 Analysis of Replicative Polymerase Usage by Ribonucleotide Incorporation (Andrea Keszthelyi, Izumi Miyabe, Katie Ptasińska, Yasukazu Daigaku, Karel Naiman, Antony M. Carr)....Pages 239-259 Dynamic Architecture of Eukaryotic DNA Replication Forks In Vivo, Visualized by Electron Microscopy (Ralph Zellweger, Massimo Lopes)....Pages 261-294 A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation (Nicolai B. Larsen, Ian D. Hickson, Hocine W. Mankouri)....Pages 295-309 Single Cell Gel Electrophoresis for the Detection of Genomic Ribonucleotides (Barbara Kind, Christine Wolf, Kerstin Engel, Alexander Rapp, M. Cristina Cardoso, Min Ae Lee-Kirsch)....Pages 311-318 Measuring the Levels of Ribonucleotides Embedded in Genomic DNA (Alice Meroni, Giulia M. Nava, Sarah Sertic, Paolo Plevani, Marco Muzi-Falconi, Federico Lazzaro)....Pages 319-327 Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing (Clinton D. Orebaugh, Scott A. Lujan, Adam B. Burkholder, Anders R. Clausen, Thomas A. Kunkel)....Pages 329-345 Detection of DNA-RNA Hybrids In Vivo (María García-Rubio, Sonia I. Barroso, Andrés Aguilera)....Pages 347-361 Analysis of De Novo Telomere Addition by Southern Blot (Diego Bonetti, Maria Pia Longhese)....Pages 363-373 Assays to Study Repair of Inducible DNA Double-Strand Breaks at Telomeres (Roxanne Oshidari, Karim Mekhail)....Pages 375-385 Telomerase RNA Imaging in Budding Yeast and Human Cells by Fluorescent In Situ Hybridization (David Guérit, Maxime Lalonde, Pascal Chartrand)....Pages 387-402 Methods to Study Repeat Fragility and Instability in Saccharomyces cerevisiae (Erica J. Polleys, Catherine H. Freudenreich)....Pages 403-419 Quantitative Analysis of the Rates for Repeat-Mediated Genome Instability in a Yeast Experimental System (Elina A. Radchenko, Ryan J. McGinty, Anna Y. Aksenova, Alexander J. Neil, Sergei M. Mirkin)....Pages 421-438 Measuring Dynamic Behavior of Trinucleotide Repeat Tracts In Vivo in Saccharomyces cerevisiae (Gregory M. Williams, Jennifer A. Surtees)....Pages 439-470 The Detection and Analysis of Chromosome Fragile Sites (Victoria A. Bjerregaard, Özgün Özer, Ian D. Hickson, Ying Liu)....Pages 471-482 Imaging of DNA Ultrafine Bridges in Budding Yeast (Oliver Quevedo, Michael Lisby)....Pages 483-493 Detection of Ultrafine Anaphase Bridges (Anna H. Bizard, Christian F. Nielsen, Ian D. Hickson)....Pages 495-508 A Chromatin Fiber Analysis Pipeline to Model DNA Synthesis and Structures in Fission Yeast (Sarah A. Sabatinos, Marc D. Green)....Pages 509-526 Long-Term Imaging of DNA Damage and Cell Cycle Progression in Budding Yeast Using Spinning Disk Confocal Microscopy (Riccardo Montecchi, Etienne Schwob)....Pages 527-536 The CellClamper: A Convenient Microfluidic Device for Time-Lapse Imaging of Yeast (Gregor W. Schmidt, Olivier Frey, Fabian Rudolf)....Pages 537-555 Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy (Alice Meroni, Federico Lazzaro, Marco Muzi-Falconi, Alessandro Podestà)....Pages 557-573 Genome-Wide Quantitative Fitness Analysis (QFA) of Yeast Cultures (Eva-Maria Holstein, Conor Lawless, Peter Banks, David Lydall)....Pages 575-597 Rewiring the Budding Yeast Proteome using Synthetic Physical Interactions (Guðjón Ólafsson, Peter H. Thorpe)....Pages 599-612 Reporter-Based Synthetic Genetic Array Analysis: A Functional Genomics Approach for Investigating Transcript or Protein Abundance Using Fluorescent Proteins in Saccharomyces cerevisiae (Hendrikje Göttert, Mojca Mattiazzi Usaj, Adam P. Rosebrock, Brenda J. Andrews)....Pages 613-629 Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA (Ryuichiro Nakato, Katsuhiko Shirahige)....Pages 631-643 Quantitative Analysis of DNA Damage Signaling Responses to Chemical and Genetic Perturbations (Francisco M. Bastos de Oliveira, Dongsung Kim, Michael Lanz, Marcus B. Smolka)....Pages 645-660 Back Matter ....Pages 661-663