R-Loops

Methods and Protocols

Andrés Aguilera, Alexey Ruzov (Herausgeber)

Buch | Softcover

470 Seiten

2023 | 1st ed. 2022
Springer-Verlag New York Inc.
978-1-0716-2479-1 (ISBN)

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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.

lt;p>1. Direct R-Loop Visualization on Genomic DNA by Native Automated Electron Microscopy

Henriette Stoy, Joel Luethi, Fabienne Roessler, Johannes Riemann, Andres Kaech, and Massimo Lopes

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

Konstantina Skourti-Stathaki

3. R-Loop Detection in Bacteria

Émilie Vlachos-Breton and Marc Drolet

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

Juan C. Cañas, Andrés Aguilera, and Belén Gómez-González

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

Junghyun Lim, Brice Laffleur, Uttiya Basu, and Kefei Yu

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

Henriette Stoy, Kevin Lang, Houra Merrikh, and Massimo Lopes

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

Susana M. Cerritelli, Kiran Sakhuja, and Robert J. Crouch

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

Sónia Silva, Cristina Guillén-Mendoza, and Andrés Aguilera

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

Marta Starczak, Abdulkadir Abakir, Alexey Ruzov, and Daniel Gackowski

10. DNA:RNA Hybrids at Telomeres in Budding Yeast

Carolin B. Wagner and Brian Luke

11. Detection of TERRA R-Loops at Human Telomeres

Galina Glousker, Rita Valador Fernandes, Marianna Feretzaki, and Joachim Lingner

12. R-Loops and Mitochondrial DNA Metabolism

Ian J. Holt

13. Highly-Purified Top1-Bound DNA Fragments

Jessica Marinello and Giovanni Capranico

14. R-Loop Immunoprecipitation: A Method to Detect R-Loop Interacting Factors In Vivo

Chiara Beghè and Natalia Gromak

15. Studies on Protein-RNA:DNA Hybrid Interactions by Microscale Thermophoresis (MST)

Miaomiao Li, Arne Klungland, and Bjørn Dalhus

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

Na Young Cheon and Ja Yil Lee

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

Haibo Yang and Li Lan

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

Khelifa Arab and Christof Niehrs

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

Adele Alagia, Ruth F. Ketley, and Monika Gullerova

20. Biochemical Analysis of RNA-DNA Hybrid and R-Loop Unwinding via Motor Proteins

Arijit Dutta, Youngho Kwon, and Patrick Sung

21. Topology of RNA:DNA Hybrids and R-Loops in Yeast

Yathish Jagadheesh Achar and Marco Foiani

22. Detecting and Mapping N6-Methyladenosine on RNA/DNA Hybrids

Abdulkadir Abakir, Fahad Alenezi, and Alexey Ruzov

23. Genome-Wide Native R-Loop Profiling by R-Loop Cleavage Under Targets and Tagmentation (R-Loop CUT&Tag)

Honghong Wang, Conghui Li, and Kaiwei Liang

24. Mapping R-Loops Using Catalytically Inactive RNaseH1 (R-ChIP)

Xuan Zhang, Yajing Hao, and Xiang-Dong Fu

25. Targeted Nuclease Approaches for Mapping Native R-Loops

Phillip Wulfridge, Qingqing Yan, and Kavitha Sarma

26. Quantitative DNA-RNA Immunoprecipitation-Sequencing with Spike-Ins

Magdalena P. Crossley and Karlene A. Cimprich

27. DNA:RNA Immunoprecipitation from S. pombe Cells for qPCR and Genome-Wide Sequencing

Laetitia Vachez, Camille Teste, and Vincent Vanoosthuyse

28. Genome-Wide Analysis of DNA-RNA Hybrids in Yeast by DRIPc-Seq and DRIP-Seq

María García-Rubio, María E. Soler-Oliva, and Andrés Aguilera

29. Quantitative, Convenient, and Efficient Genome-Wide R-Loop Profiling by ssDRIP-Seq in Multiple Organisms

Wei Xu, Kuan Li, Qin Li, Shuai Li, Jincong Zhou, and Qianwen Sun

Erscheinungsdatum	21.06.2023
Reihe/Serie	Methods in Molecular Biology
Zusatzinfo	1 Illustrations, black and white; XIV, 470 p. 1 illus.
Verlagsort	New York, NY
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Naturwissenschaften ► Biologie ► Allgemeines / Lexika
	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
	Technik ► Maschinenbau
Schlagworte	DNA-RNA hybrids • electron microscopy • Genetic diseases • Genome Dynamics • Genome-wide mapping • Genomic stress and instability • Topology
ISBN-10	1-0716-2479-2 / 1071624792
ISBN-13	978-1-0716-2479-1 / 9781071624791
Zustand	Neuware