RNA Methylation

This volume provides a comprehensive collection of current methods and protocols to study posttranscriptional base modifications in RNA with special focus on methylation. The protocols in this book discuss state-of-the-art methods for investigating aspects of RNA methylation on different types of RNA. The protocols cover topics such as wet-lab techniques for the detection of methylation, instructions for bioinformatics analyses of transcriptome-scale data, and protocols for the functional examination of RNA modifications and enzymes. Written in the highly successful Methods in 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 tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, RNA Methylation: Methods and Protocols is a valuable resource for biochemists and molecular biologists, from various fields, who wish to investigate different types of RNA methylations.

LC-MS Analysis of Methylated RNA.- Comparative Analysis of Ribonucleic Acid Digests (CARD) by mass Spectrometry.- Liquid Chromatography-Mass Spectrometry for Analysis of RNA Adenosine Methylation.- Genome-Wide Location Analyses of N6-Methyladenosine Modifications (m⁶A-seq).- Mapping m⁶A at Individual-Nucleotide Resolution using Crosslinking and Immunoprecipitation (miCLIP).- Detection and Quantification of N6-Methyladenosine in Messenger RNA by TLC.- Illustrating the Epitranscriptome at Nucleotide Resolution using Methylation-iCLIP (miCLIP).- Detection of 5-Methylcytosine in Specific Poly(A) RNAs by Bisulfite Sequencing.- Transcriptome-Wide Detection of 5-Methylcytosine by Bisulfite Sequencing.- Analysis of High-Throughput RNA Bisulfite Sequencing Data.- Statistcal Methods for Transcriptome-Wide Analysis of RNA Methylation by Bisulfite.- High-Throughput Mapping of 2'-O-Me Residues in RNA using Next-Generation Sequencing (Illumina RiboMethSeq Protocol).- RiboMeth-seq: Profiling of 2'-O-Me in RNA.- In Silico Identification of RNA Modifications from High-Throughput Sequencing Data using HAMR.- High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-seq).- Transcriptome-Wide Mapping of N¹-Methyladenosine Methylome.- In Vitro Assays for RNA Methyltransferase Activity.- Crosslinking Methods to Identify RNA Methyltransferase Targets In Vivo.- Methylated mRNA Nucleotides as Regulators for Ribosomal Translation.- Automated Chemical Solid-Phase Synthesis and Deprotection of 5-Hydroxymethylcytosine-Containing RNA.