Epitranscriptomics : methods and protocols

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. Front Matter ....Pages i-xii Bisulfite Sequencing of RNA for Transcriptome-Wide Detection of 5-Methylcytosine (Lukas Trixl, Dietmar Rieder, Thomas Amort, Alexandra Lusser)....Pages 1-21 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 et al.)....Pages 23-39 Visualization of Xist Long Noncoding RNA with a Fluorescent CRISPR/Cas9 System (Urszula Waśko, Zeming Zheng, Sanchita Bhatnagar)....Pages 41-50 HAMR: High-Throughput Annotation of Modified Ribonucleotides (Lee E. Vandivier, Zachary D. Anderson, Brian D. Gregory)....Pages 51-67 High-Resolution Mapping of N6-Methyladenosine Using m6A Crosslinking Immunoprecipitation Sequencing (m6A-CLIP-Seq) (Phillip J. Hsu, Chuan He)....Pages 69-79 Direct Chemical Biotinylation of RNA 5′-Ends Using a Diazo Reagent (Greggory M. Rice, Razvan Nutiu, Christian M. Gampe)....Pages 81-87 Identification of Methylated Transcripts Using the TRIBE Approach (Lina Worpenberg, Tobias Jakobi, Christoph Dieterich, Jean-Yves Roignant)....Pages 89-106 Decoding the Atlas of RNA Modifications from Epitranscriptome Sequencing Data (Xiao-Qin Zhang, Jian-Hua Yang)....Pages 107-124 Detection of MicroRNA-Mediated Target mRNA Cleavage and 3′-Uridylation in Human Cells by a SLA-RT-PCR Analysis (Jing Lin, Lin Ji)....Pages 125-136 Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline (Rui Dong, Xu-Kai Ma, Ling-Ling Chen, Li Yang)....Pages 137-149 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, Li-He Zhang)....Pages 151-163 Electron Microscope Detection of 5-Methylcytosine on DNA and RNA (Irene Masiello, Marco Biggiogera)....Pages 165-177 Immuno-Northern Blotting: Detection of Modified RNA Using Gel Separation and Antibodies to Modified Nucleosides (Eikan Mishima, Takaaki Abe)....Pages 179-187 LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes (Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, Runsheng Chen)....Pages 189-198 Guided Reconstruction of Full-Length Isoforms from Short Reads by CIDANE (Sandro Andreotti, Stefan Canzar)....Pages 199-208 Profiling of N6-Methyladenosine in Zika Virus RNA and Host Cellular mRNA (Gianluigi Lichinchi, Tariq M. Rana)....Pages 209-218 Detection and Quantification of Pseudouridine in RNA (Hironori Adachi, Meemanage D. DeZoysa, Yi-Tao Yu)....Pages 219-235 5-Methylcytosine Analysis by RNA-BisSeq (Yu-Sheng Chen, Hai-Li Ma, Ying Yang, Wei-Yi Lai, Bao-Fa Sun, Yun-Gui Yang)....Pages 237-248 RNA Modification Regulatory Genes in DNA Damage (Radoslav Janostiak, Narendra Wajapeyee)....Pages 249-262 Dot Blot Analysis for Measuring Global N6-Methyladenosine Modification of RNA (Arvindhan Nagarajan, Radoslav Janostiak, Narendra Wajapeyee)....Pages 263-271 Mapping and Quantification of tRNA 2′-O-Methylation by RiboMethSeq (Adeline Galvanin, Lilia Ayadi, Mark Helm, Yuri Motorin, Virginie Marchand)....Pages 273-295 Back Matter ....Pages 297-298 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.