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Genome Instability

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Marco Muzi-Falconi

    1. Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

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    You can also search for this editor in PubMed   Google Scholar

  2. Grant W Brown

    1. Donnelly Centre and Department of Biochemistry, University of Toronto, Toronto, Canada

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1672)

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Table of contents (43 protocols)

  1. Front Matter

    Pages i-xvi
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  2. The A-Like Faker Assay for Measuring Yeast Chromosome III Stability

    • Carolina A. Novoa, J. Sidney Ang, Peter C. Stirling
    Pages 1-9

  3. The Chromosome Transmission Fidelity Assay for Measuring Chromosome Loss in Yeast

    • Supipi Duffy, Philip Hieter
    Pages 11-19

  4. Measuring Mutation Rates Using the Luria-Delbrück Fluctuation Assay

    • Gregory I. Lang
    Pages 21-31

  5. Molecular Genetic Characterization of Mutagenesis Using a Highly Sensitive Single-Stranded DNA Reporter System in Budding Yeast

    • Kin Chan
    Pages 33-42

  6. Analyzing Genome Rearrangements in Saccharomyces cerevisiae

    • Anjana Srivatsan, Christopher D. Putnam, Richard D. Kolodner
    Pages 43-61

  7. High-Resolution Mapping of Modified DNA Nucleobases Using Excision Repair Enzymes

    • Monica Ransom, D. Suzi Bryan, Jay R. Hesselberth
    Pages 63-76

  8. 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

  9. 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

  10. Inserting Site-Specific DNA Lesions into Whole Genomes

    • Vincent Pagès, Robert P. Fuchs
    Pages 107-118

  11. A qPCR-Based Protocol to Quantify DSB Resection

    • Matteo Ferrari, Shyam Twayana, Federica Marini, Achille Pellicioli
    Pages 119-129

  12. Alkaline Denaturing Southern Blot Analysis to Monitor Double-Strand Break Processing

    • Chiara Vittoria Colombo, Luca Menin, Michela Clerici
    Pages 131-145

  13. Single Molecule Analysis of Resection Tracks

    • Pablo Huertas, Andrés Cruz-García
    Pages 147-154

  14. 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

  15. 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

  16. DNA Replication Profiling Using Deep Sequencing

    • Xanita Saayman, Cristina Ramos-Pérez, Grant W. Brown
    Pages 195-207

  17. Quantitative Bromodeoxyuridine Immunoprecipitation Analyzed by High-Throughput Sequencing (qBrdU-Seq or QBU)

    • Joanna E. Haye-Bertolozzi, Oscar M. Aparicio
    Pages 209-225

  18. 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

  19. Analysis of Replicative Polymerase Usage by Ribonucleotide Incorporation

    • Andrea Keszthelyi, Izumi Miyabe, Katie Ptasińska, Yasukazu Daigaku, Karel Naiman, Antony M. Carr
    Pages 239-259

  20. Dynamic Architecture of Eukaryotic DNA Replication Forks In Vivo, Visualized by Electron Microscopy

    • Ralph Zellweger, Massimo Lopes
    Pages 261-294
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Keywords

About this book

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.

Editors and Affiliations

  • Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

    Marco Muzi-Falconi

  • Donnelly Centre and Department of Biochemistry, University of Toronto, Toronto, Canada

    Grant W Brown

Bibliographic Information

  • Book Title: Genome Instability

  • Book Subtitle: Methods and Protocols

  • Editors: Marco Muzi-Falconi, Grant W Brown

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7306-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2018

  • Hardcover ISBN: 978-1-4939-7305-7Published: 20 October 2017

  • Softcover ISBN: 978-1-4939-8447-3Published: 23 August 2018

  • eBook ISBN: 978-1-4939-7306-4Published: 17 October 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 663

  • Number of Illustrations: 33 b/w illustrations, 100 illustrations in colour

  • Topics: Human Genetics

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