RNA Modifications : Methods and Protocols / edited by Mary McMahon.

Format:

Book

Contributor:

McMahon, Mary, Editor.

SpringerLink (Online service)

Series:

Springer Protocols (Springer-12345)

Methods in molecular biology 1940-6029 ; 2298

Methods in Molecular Biology, 1940-6029 ; 2298

Language:

English

Subjects (All):

Biochemistry.

Local Subjects:

Biochemistry.

Physical Description:

1 online resource (XIV, 427 pages) : 74 illustrations, 72 illustrations in color.

Edition:

1st ed. 2021.

Contained In:

Springer Nature eBook

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2021.

System Details:

text file PDF

Summary:

This detailed book describes some of the most recent advances and up-to-date methodologies to detect, quantify, analyze, and elucidate the biological function of different types of RNA modifications. Importantly, the methodologies and tools described herein can be applied to a wide variety of organisms and can be used to address biological and clinical questions. Beginning with a section on bioinformatics tools, the collection continues with sections on detecting RNA modifications using Nanopore direct RNA sequencing, next-generation sequencing approaches, qPCR- and molecular biology-based methods, mass spectrometry- and NMR-based methods, as well as approaches to assess kinetics, determinants, and functions of RNA modifications. Written for the highly successful Methods in Molecular Biology series style, chapters include introduction 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. Authoritative and practical, RNA Modifications: Methods and Protocols serves as an ideal guide for those working directly in the fields of epitranscriptomics and post-transcriptional gene regulation, as well as for scientists and clinicians interested in bioinformatic tools to study RNA modifications and techniques to dissect their roles in physiology and disease. Chapter 20 is available open access under a CC BY 4.0 license.

Contents:

RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework

An Informatics Pipeline for Profiling and Annotating RNA Modifications

EpiNano: Detection of m6A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing

Adaptation of Human Ribosomal RNA for Nanopore Sequencing of Canonical and Modified Nucleotides

AlkAniline-Seq: A Highly Sensitive and Specific Method for Simultaneous Mapping of 7-Methyl-Guanosine (m7G) and 3-Methyl-Cytidine (m3C) in RNAs by High-Throughput Sequencing

Transcriptome-Wide Detection of Internal N7-Methylguanosine

miCLIP-MaPseq Identifies Substrates of Radical SAM RNA Methylating Enzyme Using Mechanistic Crosslinking and Mismatch Profiling

Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing

Quantitative and Single Nucleotide Resolution Profiling of RNA 5-Methylcytosine

A Small RNA-Seq Protocol with Less Bias and Improved Capture of 2'-O-Methyl RNAs

Assessing 2'-O-Methylation of mRNA Using Quantitative PCR

Relative Quantification of Residue Specific m6A RNA Methylation Using m6A-RT-QPCR

Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease

Analysis of Queuosine tRNA Modifications Using APB Northern Blot Assays

Detecting ADP-Ribosylation in RNA

Detecting Internal N7-Methylguanosine mRNA Modifications by Differential Enzymatic Digestion Coupled with Mass Spectrometry Analysis

A General LC-MS-Based Method for Direct and De Novo Sequencing of RNA Mixtures Containing Both Canonical and Modified Nucleotides

Quantification of Modified Nucleosides in the Context of NAIL-MS

A Method to Monitor the Introduction of Post-Transcriptional Modifications in tRNAs with NMR Spectroscopy

Effects of mRNA Modifications on Translation: An Overview

Assaying the Molecular Determinants and Kinetics of RNA Pseudouridylation by H/ACA snoRNAs and Stand-Alone Pseudouridine Synthases

Investigating Pseudouridylation Mechanisms by High-Throughput In Vitro RNA Pseudouridylation and Sequencing

Targeted RNA m6A Editing Using Engineered CRISPR-Cas9 Conjugates.

Other Format:

Printed edition:

ISBN:

978-1-0716-1374-0

9781071613740

Access Restriction:

Restricted for use by site license.