RNA Methylation: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

Part I Modifications in abundant RNA species

1. LC-MS Analysis of Methylated RNA
Kathrin Th?ring, Katharina Schmid, Patrick Keller, and Mark Helm
2. Comparative Analysis of Ribonucleic Acid Digests (CARD) by mass SpectrometryMellie June Paulines and Patrick A. Limbach
3. Liquid Chromatography-Mass Spectrometry for Analysis of RNA Adenosine MethylationBi-Feng Yuan
Part II Analysis of N6-Methyladenosine
4. Genome-Wide Location Analyses of N6-Methyladenosine Modifications (m6A-seq)Benoit Molinie and Cosmas C. Giallourakis
5. Mapping m6A at Individual-Nucleotide Resolution using Crosslinking and Immunoprecipitation (miCLIP)Anya V. Grozhik, Bastian Linder, Anthony O. Olarerin-George, and Samie R. Jaffrey
6. Detection and Quantification of N6-Methyladenosine in Messenger RNA by TLCZsuzsanna Bodi and Rupert G. Fray
Part III Analysis of 5-Methylcytosine
7. Illustrating the Epitranscriptome at Nucleotide Resolution using Methylation-iCLIP (miCLIP)Harry George, Jernej Ule, and Shobbir Hussain
8. Detection of 5-Methylcytosine in Specific Poly(A) RNAs by Bisulfite SequencingThomas Amort and Alexandra Lusser
9. Transcriptome-Wide Detection of 5-Methylcytosine by Bisulfite SequencingThomas Amort, Xueguang Sun, Daria Cubberley, and Alexandra Lusser
10. Analysis of High-Throughput RNA Bisulfite Sequencing DataDietmar Rider and Francesca Finotello
11. Statistcal Methods for Transcriptome-Wide Analysis of RNA Methylation by BisulfiteBrian Parker
Part IV Further RNA Modifications
12. High-Throughput Mapping of 2'-O-Me Residues in RNA using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)Virginie Marchand, Lilia Ayadi, Aseel El Hajj, Florence Blanloeil-Oillo, Mark Helm, and Yuri Motorin
13. RiboMeth-seq: Profiling of 2'-O-Me in RNANicolai Krogh, Ulf Birkedal, and Henrik Nielsen
14. In Silico Identification of RNA Modifications from High-Throughput Sequencing Data using HAMRPavel P. Kuksa, Yuk Yee Leung, Lee E. Vandivier, Zachary Anderson, Brian D. Gregory, and Li-San Wang
15. High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-seq)Eva Hrabeta-Robinson, Erin Marcus, Aaron E. Cozen, Eric M. Phizicky, and Todd M. Lowe
16. Transcriptome-Wide Mapping of N1-Methyladenosine MethylomeXiaoyu Li, Jinying Peng, and Chengqi Yi
Part V Functional Assays for Modified and Unmodified RNA (17-20)
17. In Vitro Assays for RNA Methyltransferase ActivitySara Haag, Katherine E. Sloan, Claudia H?bartner, and Markus T. Bohnsack
18. Crosslinking Methods to Identify RNA Methyltransferase Targets In VivoSara Haagm Jens Kretschmer, Katherine E. Sloan, and Markus T. Bohnsack
19. Methylated mRNA Nucleotides as Regulators for Ribosomal TranslationThomas P. Hoernes and Matthias D. Erlacher
20. Automated Chemical Solid-Phase Synthesis and Deprotection of 5-Hydroxymethylcytosine-Containing RNAChristian Riml and Ronald Micura