RNA Modification Enzymes, Volume 659 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of related topics, including Locating chemical modifications in RNA sequences through ribonucleases and LC-MS based analysis, Development of RNA modification mapping pipelines for high-throughput sequencing approaches, AlkAniline-Seq for high-resolution mapping RNA m7G and m3C modifications, Facile detection of RNA phospho-methylation in cells, Detection and analysis of glycosylated queuosine modifications, A comprehensive pipeline for analysis of RNA 3'-end modification, Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry, and more.
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Table of Contents
Preface Jane E. Jackman 1. Locating chemical modifications in RNA sequences through ribonucleases and LC-MS based analysis Balasubrahmanyam Addepalli 2. Development of RNA modification mapping pipelines for high-throughput sequencing approaches Todd Lowe 3. AlkAniline-Seq for high-resolution mapping RNA m7G and m3C modifications Yuri Motorin 4. Facile detection of RNA phospho-methylation in cells Blerta Xhemalce 5. Detection and analysis of glycosylated queuosine modifications Tao Pan 6. A comprehensive pipeline for analysis of RNA 3'-end modification Inna Afasizheva 7. Analysis of the epitranscriptome with ion-pairing reagent free oligonucleotide mass spectrometry Stefanie Kellner 8. Direct sequencing (ONT) to detect m6A modification 9. RNA immunoprecipitation to identify in vivo targets of RNA editing and modifying enzymes Heather A. Hundley 10. AdoMet-based labeling of RNA Andrea Rentmeister 11. Coupling crosslinking and RNA modification sequencing for identifying RNA modification interacting proteins Juan Alfonzo 12. Characterization of codon-specific translation defects using ribosome profiling Sebastian A. Leidel 13. Partially modified tRNAs for the study of tRNA maturation and function Ute Kothe 14. In vitro assays for complex multi-step RNA modification reactions Dirk Iwata-Reuyl 15. Transient kinetic analysis for studying RNA modification enzyme mechanisms Jane E. Jackman 16. High-throughput detection and analysis of pseudouridine synthase activities Wendy Gilbert 17. Activity assays for wobble inosine modification in tRNA Dragony Fu 18. Targeting RNA with site-directed RNA Editing Josh Rosenthal 19. RNA pull-down assays for distinguishing tRNA modification substrate specificities Eric Phizicky 20. Assessing the consequences of mRNA modifications on protein synthesis using in vitro translation assays Kristin Koutmou 21. Mass spectrometry based methods for studying mRNA 5'-cap modifications Tsutomu Suzuki 22. CLIP-Seq to identify targets and interactions of RNA modification enzymes Fange Liu 23. CRISPR-mediated genome editing targeting RNA modification enzymes Douglas Bernstein
