Quantitative analysis of DNA damage signaling responses to chemical and genetic perturbations / Francisco M. Bastos de Oliveira, Dongsung Kim, Michael Lanz, and Marcus B. Smolka. Chromosome transmission fidelity assay for measuring chromosome loss in yeast / Supipi Duffy and Philip Hieter -- Measuring mutation rates using the luria-delbruck fluctuation assay / Gregory I. Lang -- Molecular genetic characterization of mutagenesis using a highly sensitive single-stranded DNA reporter system in budding yeast / Kin Chan -- Analyzing genome rearrangements in Saccharomyces cerevisiae / Anjana Srivatsan, Christopher D. Putnam, and Richard D. Kolodner -- High-resolution mapping of modified DNA nucleobases using excision repair enzymes / Monica Ransom, D. Suzi Bryan, and Jay R. Hesselberth -- 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, and Simon H. Reed -- Study of UV-induced DNA repair factor recruitment : kinetics and dynamics / Sarah Sertic, Stefania Roma, Paolo Plevani, Federico Lazzaro, and Marco Muzi-Falconi -- Inserting site-specific DNA lesions into whole genomes / Vincent Pages and Robert P. Fuchs -- qPCR-based protocol to quantify DSB resection / Matteo Ferrari, Shyam Twayana, Federica Marini, and Achille Pellicioli -- Alkaline denaturing southern blot analysis to monitor double-strand break processing / Chiara Vittoria Colombo, Luca Menin, and Michela Clerici -- Single molecule analysis of resection tracks / Pablo Huertas and Andres Cruz-Garcıa -- Mapping DNA breaks by next-generation sequencing / Laura Baranello, Fedor Kouzine, Damian Wojtowicz, Kairong Cui, Keji Zhao, Teresa M. Przytycka, Giovanni Capranico, and David Levens -- Genome-wide profiling of DNA double-strand breaks by the BLESS and BLISS methods / Reza Mirzazadeh, Tomasz Kallas, Magda Bienko, and Nicola Crosetto -- DNA replication profiling using deep sequencing / Xanita Saayman, Cristina Ramos-Perez, and Grant W. Brown -- Quantitative bromodeoxyuridine immunoprecipitation analyzed by high-throughput sequencing (qBrdU-Seq or QBU) / Joanna E. Haye-Bertolozzi and Oscar M. Aparicio -- Strand-specific analysis of DNA synthesis and proteins association with DNA replication forks in budding yeast / Chuanhe Yu, Haiyun Gan, and Zhiguo Zhang -- Analysis of replicative polymerase usage by ribonucleotide incorporation / Andrea Keszthelyi, Izumi Miyabe, Katie Ptasinska, Yasukazu Daigaku, Karel Naiman, and Antony M. Carr -- Dynamic architecture of eukaryotic DNA replication forks in vivo, visualized by electron microscopy / Ralph Zellweger and Massimo Lopes -- Molecular toolbox to engineer site-specific DNA replication perturbation / Nicolai B. Larsen, Ian D. Hickson, and Hocine W. Mankouri -- Single cell gel electrophoresis for the detection of genomic ribonucleotides / Barbara Kind, Christine Wolf, Kerstin Engel, Alexander Rapp, M. Cristina Cardoso, and Min Ae Lee-Kirsch -- Measuring the levels of ribonucleotides embedded in genomic DNA / Alice Meroni, Giulia M. Nava, Sarah Sertic, Paolo Plevani, Marco Muzi-Falconi, and Federico Lazzaro -- Mapping ribonucleotides incorporated into DNA by hydrolytic end-sequencing / Clinton D. Orebaugh, Scott A. Lujan, Adam B. Burkholder, Anders R. Clausen, and Thomas A. Kunkel -- Detection of DNA-RNA hybrids in vivo / Marıa Garcıa-Rubio, Sonia I. Barroso, and Andres Aguilera -- Analysis of de novo telomere addition by southern blot / Diego Bonetti and Maria Pia Longhese -- Assays to study repair of inducible DNA double-strand breaks at telomeres / Roxanne Oshidari and Karim Mekhail -- Telomerase RNA imaging in budding yeast and human cells by fluorescent in situ hybridization / David Guerit, Maxime Lalonde, and Pascal Chartrand -- Methods to study repeat fragility and instability in Saccharomyces cerevisiae / Erica J. Polleys and Catherine H. Freudenreich -- 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, and Sergei M. Mirkin -- Measuring dynamic behavior of trinucleotide repeat tracts in vivo in Saccharomyces cerevisiae / Gregory M. Williams and Jennifer A. Surtees -- Detection and analysis of chromosome fragile sites / Victoria A. Bjerregaard, Ozg€un Ozer, Ian D. Hickson, and Ying Liu -- Imaging of DNA ultrafine bridges in budding yeast / Oliver Quevedo and Michael Lisby -- Detection of ultrafine anaphase bridges / Anna H. Bizard, Christian F. Nielsen, and Ian D. Hickson -- Chromatin fiber analysis pipeline to model DNA synthesis and structures in fission yeast / Sarah A. Sabatinos and Marc D. Green -- Long-term imaging of DNA damage and cell cycle progression in budding yeast using spinning disk confocal microscopy / Riccardo Montecchi and Etienne Schwob -- CellClamper : a convenient microfluidic device for time-lapse imaging of yeast / Gregor W. Schmidt, Olivier Frey, and Fabian Rudolf -- Characterization of structural and configurational properties of DNA by atomic force microscopy / Alice Meroni, Federico Lazzaro, Marco Muzi-Falconi, and Alessandro Podesta -- Genome-wide quantitative fitness analysis (QFA) of yeast cultures / Eva-Maria Holstein, Conor Lawless, Peter Banks, and David Lydall -- Rewiring the budding yeast proteome using synthetic physical interactions / Guðjon O lafsson and Peter H. Thorpe -- Reporter-based synthetic genetic array analysis : a functional genomics approach for investigating transcript or protein abundance using fluorescent proteins in Saccharomyces cerevisiae / Hendrikje Gottert, Mojca Mattiazzi Usaj, Adam P. Rosebrock, and Brenda J. Andrews -- Statistical analysis and quality assessment of ChIP-seq data with DROMPA / Ryuichiro Nakato and Katsuhiko Shirahige -- Quantitative analysis of DNA damage signaling responses to chemical and genetic perturbations / Francisco M. Bastos de Oliveira, Dongsung Kim, Michael Lanz, and Marcus B. Smolka.
Summary:
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.
Series:
Methods in molecular biology, 1064-3745 ; 1672 Springer protocols, 1949-2448
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.