Small Non-Coding RNAs Methods and Protocols

This second edition provides new and updated chapters detailing methods tackling all aspects of small non-coding RNAs biology.  Chapters guide readers through customized dedicated protocols and technologies that will be of valuable help decipher the numerous functions of small non-coding RNAs. Written in the highly successful Methods of 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 key tips on  troubleshooting and avoiding known pitfalls.

Instructive and practical, Small Non-Coding RNAs: Methods and Protocols, Second Edition aims to be a valuable help and of great interest to a large number of researchers working in the field of RNA or willing to develop RNA studies.

PART I INTRODUCTION TO SMALL NON-CODING RNAS

Camille Virciglio, Yoann Abel, and Mathieu Rederstorff

2 RNA Precipitation

Valérie Bourguignon-Igel, Yoann Abel, and Mathieu Rederstorff

3 Quantitative and Qualitative Assessment of Small RNA Preparations

Virginie Marchand, Lilia Ayadi, Valérie Bourguignon-Igel, and Yuri Motorin

4 Non-coding RNA Silencing in Mammalian Cells by Antisense LNA GapmeRs Transfection

Charbel Alfeghaly, Christelle Aigueperse, Sylvain Maenner, and Isabelle Behm-Ansmant

PART II DETECTION OF SMALL NON-CODING RNAS

Jana C. Wiegard, M. Amri C. Schlüter, Olga Y. Burenina, Elena A. Kubareva, Gabriele Klug, Arnold Grünweller, and Roland K. Hartmann

6 Stem-loop qRT-PCR Based Quantification of miRNAs

Yoann Abel and Mathieu Rederstorff

7 Detection and Labeling of Small Non-coding RNAs by Splinted Ligation

Marlène Vayssières, Gabrielle Bourgeois, Florian Chardon, Anne-Sophie Tillault, and Magali Blaud

8 Fluorescence In Situ Hybridization Of Small Non-coding RNAs

Valentin Vautrot, Géraud Heckler, Christelle Aigueperse, and Isabelle Behm-Ansmant

PART III FUNCTIONAL ANALYSIS OF SMALL NON-CODING RNAS

9 Using native RIP, UV-CLIP or fCLIP to Address Protein-RNA Interactions In Vivo

Layea Baldini and Stéphane Labialle

10 Purification of RiboNucleoProtein Particles by MS2-MBP Affinity Chromatography

Aymeric Sanchez and Sylvain Maenner

11 Study of genome-wide occupancy of long non-coding RNAs using Chromatin Isolation by RNA Purification (ChIRP)

Charbel Alfeghaly, Isabelle Behm-Ansmant, and Sylvain Maenner

12 Gene Reporter Assays to Study miRNA Function

Yoann Abel and Mathieu Rederstorff

13 CRISPR/Cas9 System to Knock-Down microRNA In Vitro and In Vivo

Bin Yi, Kristina Larter, and Yaguang Xi

PART IV HIGH-THROUGHPUT ANALYSIS OF SMALL NON-CODING RNAS

14 Microarray Analysis of Whole-Transcriptome RNAs including Non-Coding RNAs

Quentin Thuillier and Isabelle Behm-Ansmant

15 Isolation, Extraction, and Deep-Sequencing Analysis Of Extracellular RNAs (exRNAs) from Human Plasma

Virginie Marchand, Adeline Galvanin, and Yuri Motorin

16 Analysis of the RNA and protein complexome by Grad-seq

Jens Hör and Jörg Vogel

17 µIVC-Seq: A Method for Ultrahigh-throughput Development and Functional Characterization of Small RNAs

Farah Bouhedda, Roger Cubi, Stéphanie Baudrey and Michael Ryckelynck

PART V STRUCTURAL APPROACHES

18 RNA Secondary Structure Study by Chemical Probing Methods using DMS and CMCT

19 Application of NMR Spectroscopy to Determine the 3D structure of Small Non-coding RNAs

Marie-Eve Chagot, Marc Quinternet, Xavier Manival, and Isabelle Lebars