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R-Loops

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Andrés Aguilera

    1. CABIMER, Universidad de Sevilla, Seville, Spain

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  2. Alexey Ruzov

    1. Skryabin Institute of Bioengineering, Research Centre of Biotechnology RAS, Moscow, Russia

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2528)

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Table of contents (29 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Direct R-Loop Visualization on Genomic DNA by Native Automated Electron Microscopy

    • Henriette Stoy, Joel Luethi, Fabienne K. Roessler, Johannes Riemann, Andres Kaech, Massimo Lopes
    Pages 1-20

  3. Detection of R-Loop Structures by Immunofluorescence Using the S9.6 Monoclonal Antibody

    • Konstantina Skourti-Stathaki
    Pages 21-29

  4. R-Loop Detection in Bacteria

    • Émilie Vlachos-Breton, Marc Drolet
    Pages 31-37

  5. Detection of R-Loops by In Vivo and In Vitro Cytosine Deamination in Saccharomyces cerevisiae

    • Juan C. Cañas, Andrés Aguilera, Belén Gómez-González
    Pages 39-53

  6. Identification of RNA–DNA Hybrids Associated with R-Loops at the IgH Switch Sequence in Activated B Cells

    • Junghyun Lim, Brice Laffleur, Uttiya Basu, Kefei Yu
    Pages 55-66

  7. Locus-Specific Analysis of Replication Dynamics and Detection of DNA–RNA Hybrids by Immuno Electron Microscopy

    • Henriette Stoy, Kevin S. Lang, Houra Merrikh, Massimo Lopes
    Pages 67-89

  8. RNase H1, the Gold Standard for R-Loop Detection

    • Susana M. Cerritelli, Kiran Sakhuja, Robert J. Crouch
    Pages 91-114

  9. RNase H1 Hybrid-Binding Domain-Based Tools for Cellular Biology Studies of DNA–RNA Hybrids in Mammalian Cells

    • Sónia Silva, Cristina Guillén-Mendoza, Andrés Aguilera
    Pages 115-125

  10. Detection and Quantification of RNA Modifications on RNA–DNA Hybrids Using SID-UPLC-MS/MS

    • Marta Starczak, Abdulkadir Abakir, Alexey Ruzov, Daniel Gackowski
    Pages 127-143

  11. DNA–RNA Hybrids at Telomeres in Budding Yeast

    • Carolin B. Wagner, Brian Luke
    Pages 145-157

  12. Detection of TERRA R-Loops at Human Telomeres

    • Galina Glousker, Rita Valador Fernandes, Marianna Feretzaki, Joachim Lingner
    Pages 159-171

  13. R-Loops and Mitochondrial DNA Metabolism

    • Ian J. Holt
    Pages 173-202

  14. Highly Purified Top1-Bound DNA Fragments

    • Jessica Marinello, Giovanni Capranico
    Pages 203-213

  15. R-Loop Immunoprecipitation: A Method to Detect R-Loop Interacting Factors

    • Chiara Beghè, Natalia Gromak
    Pages 215-237

  16. Studies on Protein–RNA:DNA Hybrid Interactions by Microscale Thermophoresis (MST)

    • Miaomiao Li, Arne Klungland, Bjørn Dalhus
    Pages 239-251

  17. Studying R-Loop Recognizing Proteins Using Single-Molecule DNA Curtain Technique and Electrophoretic Mobility Shift Assay

    • Na Young Cheon, Ja Yil Lee
    Pages 253-269

  18. Immunostaining and Protein Pull-Down of Methyl-5-Cytosine-Marked RNA:DNA Hybrids

    • Haibo Yang, Li Lan
    Pages 271-276

  19. In Vitro Binding of GADD45A to RNA:DNA Hybrids

    • Khelifa Arab, Christof Niehrs
    Pages 277-287

  20. Proximity Ligation Assay for Detection of R-Loop Complexes upon DNA Damage

    • Adele Alagia, Ruth F. Ketley, Monika Gullerova
    Pages 289-303
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Keywords

About this book

This detailed book compiles a series of laboratory protocols covering the most important aspects of R-loop biology. Beginning with a range of methods allowing for the detection of DNA-RNA hybrids, as well as their purification and visualization by electron microscopy, the volume continues with methods based on the use of RNase H-derived tools to detect DNA-RNA hybrids in vitro and in vivo. Several protocols permit studying non-canonical RNA nucleotides in the R-loop context, as well as a number of specific protocols devoted to the investigation of R-loop topology and their functional roles in the biology of mitochondria and telomeres. Finally, a large block of chapters is dedicated to different methods allowing genome-wide mapping of DNA-RNA hybrids in various organisms. Written for the highly successful Methods in Molecular Biology series, 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 practical, R-Loops: Methods and Protocols serves as an ideal resource for those working on R-loop homeostasis but also to scientists studying such areas of molecular and cell biology as genome integrity, DNA replication and repair, chromatin remodeling, transcription, RNA processing, modification and export, as well as for researchers elucidating the molecular mechanisms of cancer and genetic diseases.

Editors and Affiliations

  • CABIMER, Universidad de Sevilla, Seville, Spain

    Andrés Aguilera

  • Skryabin Institute of Bioengineering, Research Centre of Biotechnology RAS, Moscow, Russia

    Alexey Ruzov

Bibliographic Information

  • Book Title: R-Loops

  • Book Subtitle: Methods and Protocols

  • Editors: Andrés Aguilera, Alexey Ruzov

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2477-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2476-0Published: 16 June 2022

  • Softcover ISBN: 978-1-0716-2479-1Published: 17 June 2023

  • eBook ISBN: 978-1-0716-2477-7Published: 15 June 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 470

  • Number of Illustrations: 1 b/w illustrations

  • Topics: Biological Techniques, Chemistry/Food Science, general, Biomaterials, Genetics and Genomics

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