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

✍ Scribed by Haiming Cao

• Publisher: Springer US;Humana
• Year: 2021
• Tongue: English
• Leaves: 351
• Series: Methods in Molecular Biology 2254
• Edition: 1st ed.
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xiii
Bioinformatics Approaches for Functional Prediction of Long Noncoding RNAs (Fayaz Seifuddin, Mehdi Pirooznia)....Pages 1-13
Visualization of lncRNA and mRNA Structure Models Within the Integrative Genomics Viewer (Steven Busan, Kevin M. Weeks)....Pages 15-25
RNA Coding Potential Prediction Using Alignment-Free Logistic Regression Model (Ying Li, Liguo Wang)....Pages 27-39
Classification of Long Noncoding RNAs by k-mer Content (Jessime M. Kirk, Daniel Sprague, J. Mauro Calabrese)....Pages 41-60
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
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
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
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
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
Single-Cell Analysis of Long Noncoding RNAs (lncRNAs) in Mouse Brain Cells (Boyang Zhang, Wentao Xu, James Eberwine)....Pages 161-177
Detection and Characterization of Ribosome-Associated Long Noncoding RNAs (Chao Zeng, Michiaki Hamada)....Pages 179-194
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
DMS-MaPseq for Genome-Wide or Targeted RNA Structure Probing In Vitro and In Vivo (Phillip Tomezsko, Harish Swaminathan, Silvi Rouskin)....Pages 219-238
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
A Quick Immuno-FISH Protocol for Detecting RNAs, Proteins, and Chromatin Modifications (Akiyo Ogawa, Yuya Ogawa)....Pages 251-257
M(R)apping RNA–Protein Interactions (Jasmine Barra, Roberto Vendramin, Eleonora Leucci)....Pages 259-272
In Vivo Administration of Therapeutic Antisense Oligonucleotides (Luisa Statello, Mohamad Moustafa Ali, Chandrasekhar Kanduri)....Pages 273-282
CRISPR-Mediated Mutagenesis of Long Noncoding RNAs (Tomohiro Yamazaki, Tetsuro Hirose)....Pages 283-303
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
Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference (S. John Liu, Max A. Horlbeck, Jonathan S. Weissman, Daniel A. Lim)....Pages 323-338
In Vivo Functional Analysis of Nonconserved Human lncRNAs Using a Humanized Mouse Model (Yonghe Ma, Cheng-Fei Jiang, Ping Li, Haiming Cao)....Pages 339-347
Back Matter ....Pages 349-351

✦ Subjects

Life Sciences; Genetics and Genomics