R-Loops -

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Résumé :
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-Molecule DNA Curtain Technique and Electrophoretic Mobility Shift Assay.- Immunostaining and Protein Pull-Down of Methyl-5-Cytosine-Marked RNA:DNA Hybrids.- In Vitro Binding of GADD45A to RNA:DNA Hybrids.- Proximity Ligation Assay for Detection of R-Loop Complexes upon DNA Damage.- Biochemical Analysis of RNA-DNA Hybrid and R-Loop Unwinding via Motor Proteins.- Topology of RNA:DNA Hybrids and R-Loops in Yeast.- Detecting and Mapping N6-Methyladenosine on RNA/DNA Hybrids.- Genome-Wide Native R-Loop Profiling by R-Loop Cleavage Under Targets and Tagmentation (R-Loop CUT&Tag).- Mapping R-Loops Using Catalytically Inactive RNaseH1 (R-ChIP).- Targeted Nuclease Approaches for Mapping Native R-Loops.- Quantitative DNA-RNA Immunoprecipitation-Sequencing with Spike-Ins.- DNA:RNA Immunoprecipitation from S. pombe Cells for qPCR and Genome-Wide Sequencing.- Genome-Wide Analysis of DNA-RNA Hybrids in Yeast by DRIPc-Seq and DRIP-Seq.- Quantitative, Convenient, and Efficient Genome-Wide R-Loop Profiling by ssDRIP-Seq in Multiple Organisms....

Sommaire:
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.