Functional Analysis of Long Non-Coding RNAs

1. Front Matter

   Pages i-xiii

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2. Bioinformatics Approaches for Functional Prediction of Long Noncoding RNAs

   • Fayaz Seifuddin, Mehdi Pirooznia

   Pages 1-13

3. Visualization of lncRNA and mRNA Structure Models Within the Integrative Genomics Viewer

   • Steven Busan, Kevin M. Weeks

   Pages 15-25

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

   • Ying Li, Liguo Wang

   Pages 27-39

5. Classification of Long Noncoding RNAs by k-mer Content

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

   Pages 41-60

6. Genome-Wide Computational Analysis and Validation of Potential Long Noncoding RNA-Mediated DNA–DNA–RNA Triplexes in the Human Genome

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

   Pages 61-71

7. Using INFERNO to Infer the Molecular Mechanisms Underlying Noncoding Genetic Associations

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

   Pages 73-91

8. A Bioinformatic Pipeline to Integrate GWAS and eQTL Datasets to Identify Disease Relevant Human Long Noncoding RNAs

   • Yi Chen, Ping Li, Haiming Cao

   Pages 93-110

9. AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs

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

   Pages 111-131

10. Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS)

    • Sílvia Carbonell Sala, Barbara Uszczyńska-Ratajczak, Julien Lagarde, Rory Johnson, Roderic Guigó

    Pages 133-159

11. Single-Cell Analysis of Long Noncoding RNAs (lncRNAs) in Mouse Brain Cells

    • Boyang Zhang, Wentao Xu, James Eberwine

    Pages 161-177

12. Detection and Characterization of Ribosome-Associated Long Noncoding RNAs

    • Chao Zeng, Michiaki Hamada

    Pages 179-194

13. Analysis of Annotated and Unannotated Long Noncoding RNAs from Exosome Subtypes Using Next-Generation RNA Sequencing

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

    Pages 195-218

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

    • Phillip Tomezsko, Harish Swaminathan, Silvi Rouskin

    Pages 219-238

15. 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, Chandrasekhar Kanduri

    Pages 239-249

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

    • Akiyo Ogawa, Yuya Ogawa

    Pages 251-257

17. M(R)apping RNA–Protein Interactions

    • Jasmine Barra, Roberto Vendramin, Eleonora Leucci

    Pages 259-272

18. In Vivo Administration of Therapeutic Antisense Oligonucleotides

    • Luisa Statello, Mohamad Moustafa Ali, Chandrasekhar Kanduri

    Pages 273-282

19. CRISPR-Mediated Mutagenesis of Long Noncoding RNAs

    • Tomohiro Yamazaki, Tetsuro Hirose

    Pages 283-303

20. In Vivo CRISPR/Cas9-Based Targeted Disruption and Knockin of a Long Noncoding RNA

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

    Pages 305-321

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 atimely 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.

• RNA dysfunction
• Novel therapeutic targets
• lncRNAs
• Bioinformatics
• Functional analysis
• Disease-associated human lncRNAs
• Pathophysiology

• Cardiovascular Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, USA

  Haiming Cao

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