Rna-Chromatin Interactions: Methods and Protocols

ISBN-13: 9781071606797 / Angielski / Twarda / 2020 / 266 str.

Ulf Andersson Vang Ørom

Spis treści

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

Célia Carvalho and Maria Carmo-Fonseca

 

5. Targeting Polyadenylation for Retention of RNA at Chromatin

Evgenia Ntini and Ulf Andersson Vang Ørom

 

_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

Jörg 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 Längst

  

18. Mapping RNA-chromatin interactions in vivo with RNA-DamID

Seth W. Cheetham and Andrea H. Brand

 

Blurb

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.