Functional Analysis of Long Non-Coding RNAs: Methods and Protocols

ISBN-13: 9781071611609 / Angielski / Miękka / 2021

Cao, Haiming

Opis

This detailed volume presents a comprehensive bioinformatic and experimental toolbox for prioritizing, annotating, and functionally analyzing long non-coding RNAs (lncRNAs). Playing a vital role in diverse biological progresses and human disease, lncRNAs have proven to be a challenging subject of study due to our limited understanding of their sequence-function relationships, lack of complete genetic annotation, and the unavailability of systems required to define their functional importance and molecular mechanisms, all of which this book seeks to address. 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. 

Authoritative and practical, Functional Analysis of Long Non-Coding RNAs: Methods and Protocols provides a timely and convenient resource to facilitate the identification and characterization of disease-associated human lncRNAs, which aims to shed light on their role in biology and pathophysiology and ultimately lead toward novel therapeutic approaches targeting lncRNAs for the amelioration of human diseases.

Spis treści

1. Bioinformatics Approaches for Functional Prediction of Long Non-Coding RNAs

            Fayaz Seifuddin and Mehdi Pirooznia

 

2. Visualization of lncRNA and mRNA Structure Models within the Integrative Genomics Viewer

            Steven Busan and Kevin M. Weeks

 

3. RNA Coding Potential Prediction Using Alignment-Free Logistic Regression Model

            Ying Li and Liguo Wang

 

4. Classification of Long Non-Coding RNAs by K-mer Content

            Jessime M. Kirk, Daniel Sprague, and J. Mauro Calabrese

 

5. Genome-Wide Computational Analysis and Validation of Potential Long Non-Coding RNA-Mediated DNA-DNA:RNA Triplexes in the Human Genome

            Saakshi Jalali, Amrita Singh, Vinod Scaria, and Souvik Maiti

 

6. Using INFERNO to Infer the Molecular Mechanisms Underlying Non-Coding Genetic Associations

            Alexandre Amlie-Wolf, Pavel P. Kuksa, Chien-Yueh Lee, Elisabeth Mlynarski, Yuk Yee Leung, and Li-San Wang

 

7. A Bioinformatic Pipeline to Integrate GWAS and eQTL Datasets to Identify Disease Relevant Human Long Non-Coding RNAs

            Yi Chen, Ping Li, and Haiming Cao

 

8. AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Non-Coding RNAs

            De-Chang Yang, Lan Ke, Yang Ding, and Ge Gao

 

9. Annotation of Full-Length Long Non-Coding RNAs with Capture Long-Read Sequencing (CLS)

            Silvia Carbonell Sala, Barbara Uszczyńska-Ratajczak, Julien Lagarde, Rory Johnson, and Roderic Guigo

 

10. Single-Cell Analysis of Long Non-Coding RNAs (lncRNAs) in Mouse Brain Cells

            Boyang Zhang, Wentao Xu, and James Eberwine

 

11. Detection and Characterization of Ribosome-Associated Long Non-Coding RNAs

            Chao Zeng and Michiaki Hamada

 

12. Analysis of Annotated and Unannotated Long Non-Coding RNAs from Exosome Subtypes Using Next-Generation RNA Sequencing

            Wittaya Suwakulsiri, Maoshan Chen, David W. Greening, Rong Xu, and Richard J. Simpson

 

13. DMS-MaPseq for Genome-Wide or Targeted RNA Structure Probing In Vitro and In Vivo

            Phillip Tomezsko, Harish Swaminathan, and Silvi Rouskin

 

14. Labeling and Purification of Temporally Expressed RNAs during the S-Phase of the Cell Cycle in Living Cells

            Matthieu Meryet-Figuiere, Mohamad Moustafa Ali, Santhilal Subhash, and Chandrasekhar Kanduri

 

15. A Quick Immuno-FISH Protocol for Detecting RNAs, Proteins, and Chromatin Modifications

            Akiyo Ogawa and Yuya Ogawa

 

16. M(R)apping RNA-Protein Interactions

            Jasmine Barra, Roberto Vendramin, and Eleonora Leucci

 

17. In Vivo Administration of Therapeutic Antisense Oligonucleotides

            Luisa Statello, Mohamad Moustafa Ali, and Chandrasekhar Kanduri

 

18. CRISPR-Mediated Mutagenesis of Long Non-Coding RNAs

            Tomohiro Yamazaki and Tetsuro Hirose

 

19. In Vivo CRISPR/Cas9-Based Targeted Disruption and Knock-In of a Long Non-Coding RNA

            Xi Cheng, Samuel T. Peters, Shondra M. Pruett-Miller, Thomas Saunders, and Bina Joe

 

20. Genome-Scale Perturbation of Long Non-Coding RNA Expression Using CRISPR Interference

            S. John Liu, Max A. Horlbeck, Jonathan S. Weissman, and Daniel A. Lim

 

21. In Vivo Functional Analysis of Non-Conserved Human lncRNAs Using a Humanized Mouse Model

            Yonghe Ma, Cheng-fei Jiang, Ping Li, and Haiming Cao