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This volume focuses on RNAs interacting with chromatin and their function. Chapters guide readers through transcription, splicing, non-coding RNA function and manipulation of gene expression. 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, RNA-Chromatin Interactions: Methods and Protocols aims to be a starting-point to expand researchers experimental approaches towards the numerous outstanding questions in this new and expanding field.
List of contents
Tuning the Expression of Long Noncoding RNA loci with CRISPR Interference.- Identification of Chromatin binding sites for Long noncoding RNAs by Chromatin Oligo Affinity Precipitation (ChOP).- Knock-down of Nuclear lncRNAs by Locked Nucleic Acid (LNA) Gapmers in Nephron Progenitor Cells.- Design and Application of a Short (16-mer) Locked Nucleic Acid splice-Switching Oligonucleotide for Dystrophin Production in Duchenne Muscular Dystrophy Myotubes.- Targeting Polyadenylation for Retention of RNA at Chromatin.- Simultaneous Detection of RNAs and Proteins with Subcellular Resolution.- In Vivo Crosslinking of Histone and RNA-binding Proteins.- Proteomics-based Systematic Identification of Nuclear Proteins Anchored to Chromatin via RNA.- 2D Saturation Transfer Difference NMR for Determination of Protein Binding Sites on RNA Guanine Quadruplexes.- Mapping Transcriptome-wide and Genome-wide RNA-DNA Contacts with Chromatin-Associated RNA Sequencing (ChAR-seq).- Identification of cis-elements for RNA Subcellular Localization through REL-seq.- Transcriptome-wide Mapping of Protein-RNA Interactions.- Proximity RNA-seq, A Sequencing Method to Identify Co-localization of RNA.- Immunoprecipitation of DNA-RNA Hybrids using the S9.6 Antibody.- Characterization of R-loop Structures using Single-Molecule R-loop Footprinting and Sequencing.- Characterization of R-loop Structures using Single-Molecule R-loop Footprinting and Sequencing.- Analyzing RNA-DNA Triplex Formation in Chromatin.- Mapping RNA-chromatin interactions in vivo with RNA-DamID.
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