RNA-Chromatin Interactions Methods and Protocols Preface

1. Tuning the Expression of Long Noncoding RNA loci with CRISPR Interference Lovorka Stojic 2. Identification of Chromatin binding sites for Long noncoding RNAs by Chromatin Oligo Affinity Precipitation (ChOP) Marianna Nicoletta Rossi and Rossella Maione 3. Knock-down of Nuclear lncRNAs by Locked Nucleic Acid (LNA) Gapmers in Nephron Progenitor Cells Masaki Nishikawa and Norimoto Yanagawa 4. Design and Application of a Short (16-mer) Locked Nucleic Acid splice-Switching Oligonucleotide for Dystrophin Production in Duchenne Muscular Dystrophy Myotubes Celia Carvalho and Maria Carmo-Fonseca 5. Targeting Polyadenylation for Retention of RNA at Chromatin Evgenia Ntini and Ulf Andersson Vang Orom 6. Simultaneous Detection of RNAs and Proteins with Subcellular Resolution Sunjong Kwon, Koei Chin, and Michel Nederlof 7. In Vivo Crosslinking of Histone and RNA-binding Proteins Yong-Eun Kim, Kyoon Eon Kim, and Kee K. Kim 8. Proteomics-based Systematic Identification of Nuclear Proteins Anchored to Chromatin via RNA Kyoko Hiragami-Hamada, Naoki Tani, and Jun-ichi Nakayama 9. 2D Saturation Transfer Difference NMR for Determination of Protein Binding Sites on RNA Guanine Quadruplexes Ewan K.S. McRae, David E. Davidson, and Sean A. McKenna 10. Mapping Transcriptome-wide and Genome-wide RNA-DNA Contacts with Chromatin-Associated RNA Sequencing (ChAR-seq) Charles Limouse, David Jukam, Owen K. Smith, Kelsey Fryer, and Aaron F. Straight 11. Identification of cis-elements for RNA Subcellular Localization through REL-seq Yafei Yin and Xiaohua Shen 12. Transcriptome-wide Mapping of Protein-RNA Interactions Xianju Bi and Xiaohua Shen 13. Proximity RNA-seq, A Sequencing Method to Identify Co-localization of RNA Joerg Morf and Steven W. Wingett 14. Immunoprecipitation of DNA-RNA Hybrids using the S9.6 Antibody Hunter R. Gibbons and Thomas M. Aune 15. Characterization of R-loop Structures using Single-Molecule R-loop Footprinting and Sequencing Maika Malig and Frederic Chedin 16. Characterization of R-loop Structures using Single-Molecule R-loop Footprinting and Sequencing Maika Malig and Frederic Chedin 17. Analyzing RNA-DNA Triplex Formation in Chromatin Rodrigo Maldonado and Gernot Langst 18. Mapping RNA-chromatin interactions in vivo with RNA-DamID Seth W. Cheetham and Andrea H. Brand