R-Loops: methods and protocols

by Aguilera, Andrés Ruzov, Alexey

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Title Statements

Full title :R-Loops : methods and protocols / edited by Andrés Aguilera, Alexey Ruzov.

Summary

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.

Edition Statements

Publication Date:2022

Publication Statements

Publisher(s):Humana Press
Place of Publication:New York, NY
Language:eng
Publication Date:2022

The Physical Object

Description:xiv, 470 pages : : illustrations (some color) ; : 26 cm.

Edition Identifiers

ISBN:9781071624760, 1071624768
oclc:on1302580949
LC Classification:QP623.8.P75
Dewey Decimal:572.88

Direct R-Loop Visualization on Genomic DNA by Native Automated Electron Microscopy -- Detection of R-Loop Structures by Immunofluorescence Using the S9.6 Monoclonal Antibody -- R-Loop Detection in Bacteria -- Detection of R-Loops by In Vivo and In Vitro Cytosine Deamination in Saccharomyces cerevisiae -- Identification of RNA-DNA Hybrids Associated with R-Loops at the IgH Switch Sequence in Activated B Cells -- Locus-Specific Analysis of Replication Dynamics and Detection of DNA:RNA Hybrids by Immuno Electron Microscopy -- RNase H1, the Gold Standard for R-Loop Detection -- RNase H1 Hybrid-Binding Domain-Based Tools for Cellular Biology Studies of DNA-RNA Hybrids in Mammalian Cells -- Detection and Quantification of RNA Modifications on RNA/DNA Hybrids Using SID-UPLC-MS/MS -- DNA:RNA Hybrids at Telomeres in Budding Yeast -- Detection of TERRA R-Loops at Human Telomeres -- R-Loops and Mitochondrial DNA Metabolism -- Highly-Purified Top1-Bound DNA Fragments -- R-Loop Immunoprecipitation: A Method to Detect R-Loop Interacting Factors In Vivo -- Studies on Protein-RNA:DNA Hybrid Interactions by Microscale Thermophoresis (MST) -- Studying R-Loop Recognizing Proteins Using Single-Molecu…