PART I INTRODUCTION TO SMALL NON-CODING RNAS
1 Regulatory Non-coding RNAs: An Overview
Camille Virciglio, Yoann Abel, and Mathieu Rederstorff
2 RNA Precipitation
Valerie Bourguignon-Igel, Yoann Abel, and Mathieu Rederstorff
3 Quantitative and Qualitative Assessment of Small RNA Preparations
Virginie Marchand, Lilia Ayadi, Valerie 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
5 Northern Blot Detection of Tiny RNAs
Jana C. Wiegard, M. Amri C. Schluter, Olga Y. Burenina, Elena A. Kubareva, Gabriele Klug, Arnold Grunweller, 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
Marlene Vayssieres, Gabrielle Bourgeois, Florian Chardon, Anne-Sophie Tillault, and Magali Blaud
8 Fluorescence In Situ Hybridization Of Small Non-coding RNAs
Valentin Vautrot, Geraud 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 Stephane 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 Hoer and Joerg Vogel
17 IVC-Seq: A Method for Ultrahigh-throughput Development and Functional Characterization of Small RNAs
Farah Bouhedda, Roger Cubi, Stephanie Baudrey and Michael Ryckelynck
PART V STRUCTURAL APPROACHES
18 RNA Secondary Structure Study by Chemical Probing Methods using DMS and CMCT
Fatima Alghoul, Gilbert Eriani, and Franck Martin
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
