Epitranscriptomics: Methods and Protocols

ISBN-13: 9781493988075 / Angielski / Twarda / 2018 / 298 str.

Narendra Wajapeyee; Romi Gupta

Spis treści

Preface…

Table of Contents…

Contributing Authors…

1. Bisulfite Sequencing of RNA for Transcriptome-Wide Detection of 5-Methylcytosine

Lukas Trixl, Dietmar Rieder, Thomas Amort, and Alexandra Lusser

2. Single-Molecule Analysis of RNA Dynamics in Living Cells Using Molecular Beacons

Mingming Chen, Shiqi Mao, Xiaotian Wu, Zhao Ma, Yantao Yang, Christopher J. Krueger, and Antony K. Chen

3. Visualization of Xist Long Non-Coding RNA with Fluorescent CRISPR/CAS9 System

Urszula Waśko, Zeming Zheng, and Sanchita Bhatnagar

4. HAMR: High-Throughput Annotation of Modified Ribonucleotides

Lee E. Vandivier, Zachary D. Anderson, and Brian D. Gregory

5. High-Resolution Mapping of N6-Methyladenosine Using m6A Crosslinking Immunoprecipitation Sequencing (m6A-CLIP-seq)

Phillip J. Hsu and Chuan He

6. Direct Chemical Biotinylation of RNA 5’-Ends Using a Diazo Reagent

Greggory M. Rice, Razvan Nutiu, and Christian M. Gampe

7. Identification of Methylated Transcripts Using the TRIBE Approach

Lina Worpenberg, Tobias Jakobi, Christoph Dieterich, and Jean-Yves Roignant

8. Decoding the Atlas of RNA Modifications from Epitranscriptome Sequencing Data

Xiao-qin Zhang and Jian-hua Yang

9. Detection of MicroRNA-Mediated Target mRNA Cleavage and 3'-Uridylation in Human Cells by a SLA-RT-PCR Analysis

Jing Lin and Lin Ji

10. Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline

Rui Dong, Xu-Kai Ma, Ling-Ling Chen, and Li Yang

11. Synthesis and Evaluation of Novel Neamine-Nucleoside Conjugates as Potential Antibiotic Targets for Escherichia coli 16S Ribosomal RNA

Zhen-Jun Yang, Maria-Grazia Concilio, Vasudevan Ramesh, and Li-He Zhang

12. Electron Microscope Detection of 5-Methylcytosine on DNA and RNA

Irene Masiello and Marco Biggiogera

13. Immuno-Northern Blotting: Detection of Modified RNA Using Gel Separation and Antibodies to Modified Nucleosides

Eikan Mishima and Takaaki Abe

14. LncVar：Deciphering Genetic Variations Associated with Long Non-Coding Genes

Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, and Runsheng Chen

15. Guided Reconstruction of Full-Length Isoforms from Short Reads by CIDANE

Sandro Andreotti and Stefan Canzar

16. Profiling of N6-Methyladenosine in Zika Virus RNA and Host Cellular mRNA

Gianluigi Lichinchi and Tariq M. Rana

17. Detection and Quantification of Pseudouridine in RNA

Hironori Adachi, Meemanage D. DeZoysa, and Yi-Tao Yu

18. 5-Methylcytosine Analysis by RNA-BisSeq

Yu-Sheng Chen, Hai-Li Ma, Ying Yang, Wei-Yi Lai, Bao-Fa Sun, and Yun-Gui Yang

19. RNA Modification Regulatory Genes in DNA Damage

Radoslav Janostiak and Narendra Wajapeyee

20. Dot Blot Analysis for Measuring Global N6-Methyladenosine Modification of RNA

Arvindhan Nagarajan, Radoslav Janostiak, and Narendra Wajapeyee

Blurb

This volume provides readers with the latest technologies to study changes in the epitranscriptome. The protocols described in this book explore both targeted and unbiased high-throughput analysis associated with post-transcriptional RNA modification. The chapters in this book also cover specific topics such as transcriptome-wide detection of 5-methylcytosine; HAMR; iRNA-2OM; genome-wide annotation of circRNAs; immune-northern blotting; and detection and quantification of pseudouridine in RNA. 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.

Authoritative and comprehensive, Epitranscriptomics: Methods and Protocols is an important resource for both expert and novice scientists who are interested in learning more about this field.