Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
This volume focuses on RNAs interacting with chromatin and their function. Chapters guide readers through tranillegalscription, 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.
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 Tranillegalscriptome-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. Tranillegalscriptome-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
This volume focuses on RNAs interacting with chromatin and their function. Chapters guide readers through tranillegalscription, 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.
This volume focuses on RNAs interacting with chromatin and their function. Chapters guide readers through tranillegalscription, 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.
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 Tranillegalscriptome-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.- Tranillegalscriptome-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.
Über den Autor
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Inhaltsverzeichnis
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 Tranillegalscriptome-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. Tranillegalscriptome-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
Klappentext
This volume focuses on RNAs interacting with chromatin and their function. Chapters guide readers through tranillegalscription, 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.
n
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.
n
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
