Main 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.

Contents:

1. The A-like Faker Assay for Measuring Yeast Chromosome III Stability

Carolina A. Novoa, J. Sidney Ang, and Peter C. Stirling

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

Supipi Duffy and Philip Hieter

3. Measuring Mutation Rates using the Luria-Delbruck Fluctuation Assay

Gregory I. Lang

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

Kin Chan

5. Analyzing Genome Rearrangements in Saccharomyces cerevisiae

Anjana Srivatsan, Christopher D. Putnam, and Richard D. Kolodner

6. High Resolution Mapping of Modified DNA Nucleobases using Excision Repair Enzymes

Monica Ransom, D. Suzi Bryan and Jay R. Hesselberth

7. 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

8. Study of UV-induced DNA Repair Factor Recruitment: Kinetics and Dynamics

Sertic S., Roma S., Plevani P., Lazzaro F. , and Muzi-Falconi M.

9. Inserting Site-specific DNA Lesions into Whole Genomes

Vincent Pages and Robert P Fuchs

10. A qPCR-based Protocol to Quantify DSB Resection

Matteo Ferrari, Shyam Twayana, Federica Marini, and Achille Pellicioli

11. Alkaline Denaturing Southern Blot Analysis to Monitor Double-strand Break Processing

Chiara Vittoria Colombo, Luca Menin, and Michela Clerici

12. Single Molecule Analysis of Resection Tracks

Pablo Huertas and Andres Cruz-Garcia

13. 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

14. Genome-wide Profiling of DNA Double-strand Breaks by the BLESS and BLISS Methods

Reza Mirzazadeh, Tomasz Kallas, Magda Bienko, and Nicola Crosetto

15. DNA Replication Profiling using Deep Sequencing

Xanita Saayman, Cristina Ramos-Perez, and Grant W Brown

16. Quantitative Bromodeoxyuridine Immunoprecipitation Analyzed by High-Throughput Sequencing (qBrdU-seq or QBU)

Joanna E. Haye-Bertolozzi and Oscar M. Aparicio

17. Strand-specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast

Chuanhe Yu, Haiyun Gan, and Zhiguo Zhang

18. Analysis of Replicative Polymerase Usage by Ribonucleotide Incorporation

Andrea Keszthelyi, Izumi Miyabe, Katie Ptasinska, Yasukazu Daigaku, Karel Naiman, and Antony M. Carr

19. Dynamic Architecture of Eukaryotic DNA Replication Forks in vivo, Visualized by Electron Microscopy

Ralph Zellweger and Massimo Lopes

20. A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation

Nicolai B. Larsen, Ian D. Hickson, and Hocine W. Mankouri

21. 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

22. Measuring the Levels of Ribonucleotides Embedded in Genomic DNA

Meroni A., Nava G.M., Sertic S., Plevani P., Muzi-Falconi M. and Lazzaro F.

23. 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

24. Detection of DNA-RNA Hybrids in vivo

Maria Garcia-Rubio, Sonia I. Barroso, and Andres Aguilera

25. Analysis of de novo Telomere Addition by Southern Blot

Diego Bonetti and Maria Pia Longhese

26. Assays to Study Repair of Inducible DNA Double Strand Breaks at Telomeres

Roxanne Oshidari and Karim Mekhail

27. Telomerase RNA Imaging in Budding Yeast and Human Cells by Fluorescent in situ Hybridization

David Guerit, Maxime Lalonde, and Pascal Chartrand

28. Methods to Study Repeat Fragility and Instability in Saccharomyces cerevisiae

Erica J. Polleys and Catherine H. Freudenreich

29. 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. Mirkin1

30. Measuring Dynamic Behaviour of Trinucleotide Repeat Tracts in vivo in Saccharomyces cerevisiae

Gregory M. Williams and Jennifer A. Surtees

31. The Detection and Analysis of Chromosome Fragile Sites

Victoria A. Bjerregaard, OEzgun OEzer, Ian D. Hickson, and Ying Liu

32. Imaging of DNA Ultrafine Bridges in Budding Yeast

Oliver Quevedo and Michael Lisby

33. Detection of Ultra-Fine Anaphase Bridges

Anna H. Bizard, Christian F. Nielsen, and Ian D. Hickson

34. A Chromatin Fiber Analysis Pipeline to Model DNA Synthesis and Structures in Fission Yeast

Sarah A. Sabatinos and Marc D. Green

35. Long-term Imaging of DNA Damage and Cell Cycle Progression in Budding Yeast Using Spinning Disk Confocal Microscopy

Riccardo Montecchi and Etienne Schwob

36. The CellClamper: A Convenient Microuidic Device for Time-Lapse Imaging of Yeast

Gregor W. Schmidt, Olivier Frey, and Fabian Rudolf

37. Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy Alice Meroni, Federico Lazzaro, Marco Muzi-Falconi, and Alessandro Podesta

38. Genome-wide Quantitative Fitness Analysis (QFA) of Yeast Cultures

Eva-Maria Holstein, Conor Lawless, Peter Banks, and David Lydall

39. Rewiring the Budding Yeast Proteome using Synthetic Physical Interactions

Gudjon Olafsson and Peter H. Thorpe

40. Reporter-based Synthetic Genetic Array Analysis: a Functional Genomics Approach for Investigating Transcript or Protein Abundance Using Fluorescent Proteins in Saccharomyces cerevisiae

Hendrikje Goettert, Mojca Mattiazzi Usaj, Adam P. Rosebrock, and Brenda J. Andrews

41. Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA

Ryuichiro Nakato and Katsuhiko Shirahige

42. 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