RNA modification:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elesevier, Acad. Press
2015
|
| Edition: | 1. ed. |
| Series: | Methods in enzymology
560 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVIII, 409 S., [6] Bl. Ill., graph. Darst. |
| ISBN: | 9780128021927 |
Staff View
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| 245 | 1 | 0 | |a RNA modification |c ed. by Chuan He |
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Record in the Search Index
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| adam_text | Titel: RNA modification
Autor: He, Chuan
Jahr: 2015
CONTENTS
Contributors xi
Preface xvii
1. Methodology for the High-Throughput Identification
and Characterization of tRNA Variants That Are Substrates
for a tRNA Decay Pathway 1
Matthew J. Payea, Michael P. Guy, arid Eric M. Phizicky
1. Introduction 2
2. High-Throughput Identification of tRNA Substrates Degraded
by the RTD Pathway 4
3. Measurement of tRNA Levels of RTD Substrate SUP4oc Variants
in the Presence of WT tRNATyr 8
4. Conclusions and Additional Applications of These Approaches 13
Acknowledgments 15
References 16
2. Nucleoside Analysis by Hydrophilic Interaction Liquid
Chromatography Coupled with Mass Spectrometry 19
Yuriko Sakaguchi, Kenjyo Miyauchi, Byeong-il Kang, and Tsutomu Suzuki
1. Introduction 20
2. Nucleoside Preparation for LC/MS Analysis 21
3. HIUC/ESI-MS for Total Nucleosides 22
4. HIUC/ESI-MS Versus RPC/ESI-MS for Nucleoside Analysis 22
5. Profiling of Modified Nucleosides in HIUC/ESI-MS 23
6. Discussion 26
Acknowledgments 26
References 27
3. A Platform for Discovery and Quantification of Modified
Ribonucleosides in RNA: Application to Stress-Induced
Reprogramming of tRNA Modifications 29
Weiling Maggie Cai, Yok Hian Chionh, Fabian Hia, Chen Gu, Stefanie Kellner,
Megan E. McBee, Chee Sheng Ng, Yan Ling Joy Pang, Erin G. Prestwich,
Kok Seong Lim, I. Ramesh Babu, Thomas J. Begley, and Peter C. Dedon
1. Introduction 30
vi
Contents
2. Methods 32
3. Discussion 61
Acknowledgments 64
References 64
4. Recognition of Specified RNA Modifications by the Innate
Immune System 73
Tatjana Eigenbrod, Patrick Keller, Steffen Kaiser, Katharina Rimbach,
Alexander H. Dalpke, and Mark Helm
1. Introduction 74
2. Preparation of tRNA Modivariants 77
3. Preparation and Stimulation of Human PBMC 83
4. Preparation of Human PBMCs 84
5. Stimulation of Human PBMC 85
Acknowledgment 87
References 87
5. Kinetic Analysis of tRNA Methyltransferases 91
Va-Ming Hou and Isao Masuda
1. Introduction 92
2. Methodology 99
3. Steady-State Assays 99
4. Pre-Steady-State Assays 104
5. Single-Turnover Assays 109
6. Conclusions 113
Acknowledgments 113
References 113
6. Preparation of Human Nuclear RNA m6A Methyltransferases
and Demethylases and Biochemical Characterization
of Their Catalytic Activity 117
Jianzhao Liu, Yanan Yue, and Chuan He
1. Introduction 118
2. Expression of Human Nuclear RNA m6A Methyltransferase
Core Complex METTL3-METTL14-WTAP in Insect Cell
Expression System 119
3. Expression of Human Nuclear RNA m6A Demethylases
FTO and ALKBH5 122
Contents
vii
4. Biochemical Characterization of the Catalytic Activity of the m6A
Methyltransferases and Demethylases 123
5. Conclusions 129
Acknowledgments 129
References 129
7. Transcriptome-Wide Mapping of A^-Methyladenosine
by m6A-Seq 131
Dan Dominissini, Sharon Moshitch-Moshkovitz, Ninette Amariglio,
and Gideon Rechavi
1. Theory 132
2. Equipment 134
3. Materials 134
4. Protocol 138
5. Step 1: RNA Preparation and Fragmentation 139
6. Step 2: RNA Immunoprecipitation 142
7. Step 3: Library Preparation and Deep Sequencing 145
Acknowledgments 146
References 146
8. Probing RNA Modification Status at Single-Nucleotide
Resolution in Total RNA 149
Nian Liu and Tao Pan
1. Introduction 150
2. Methods 151
3. Notes 156
Acknowledgments 157
References 157
9. High-Resolution Mapping of N^Methyladenosine
in Transcriptome and Genome Using a
Photo-Crosslinking-Assisted Strategy 161
Kai Chen, Guan-Zheng Luo, and Chuan He
1. Introduction 162
2. Equipment 166
3. Materials 168
4. Protocol 1: Photo-Crosslinking-Assisted msA Sequencing 173
5. Protocol 2: 6mA-CLIP-exo Sequencing 176
viii
Contents
6. Conclusion 182
Acknowledgments 182
References 182
10. Pseudouridine in mRNA: Incorporation, Detection,
and Recoding 187
Guowei Wu, Chao Huang, and Yi-Tao Yu
1. Introduction 188
2. Incorporation of Pseudouridine in TRM4 mRNA 190
3. Detection of Pseudouridine in the TRM4 mRNA 202
4. Recoding of Pseudouridylated PTC Codon 212
Acknowledgments 216
References 216
11. Pseudo-Seq: Genome-Wide Detection of Pseudouridine
Modifications in RNA 219
Thomas M. Carlile, Maria F. Rojas-Duran, and Wendy V. Gilbert
1. Introduction 220
2. Sample Preparation and RNA Isolation 223
3. Pseudo-Seq Library Preparation 227
4. Pseudo-Seq Data Analysis 235
5. Experimental Considerations 239
6. Solutions, Reagents, and Common Protocols 241
Acknowledgments 243
References 243
12. Pseudouridine Chemical Labeling and Profiling 247
Xiaoyu Li, Shiqing Ma, and Chengqi Yi
1. Theory 248
2. Equipment 249
3. Materials 249
4. Protocol 252
5. Step 1: Total RNA Isolation from Mammalian
Tissues and Cells 254
6. Step 2: mRNA Isolation 255
7. Step 3: N3-CMC Labeling and Click Reaction 258
8. Step 4: Enrich rjr-Containing RNA Fragments by Streptavidin
Pull Down 260
9. Step 5: RNA Ligation 261
Contents
ix
10. Step 6: Reverse Transcription 265
11. Step 7: Circligation, Linearization, and PCR Amplification 267
References 271
13. Experimental Approaches for Target Profiling
of RNA Cytosine Methyltransferases 273
Vahid Khoddami, Archana Yerra, and Bradley R. Cairns
1. Introduction 274
2. Methods 277
References 294
14. RNA 5-Methylcytosine Analysis by Bisulfite Sequencing 297
Matthias Schaefer
1. Introduction 298
2. Methods for Identifying m5C-Modified RNA in Sequence Context 305
3. Considerations Before RNA Bisulfite Sequencing (RNA-BisSeq) 308
4. General Protocol for RNA-BisSeq 314
5. RNA-BisSeq Data Analysis 320
6. Limitations of RNA-BisSeq 321
Acknowledgments 322
References 323
15. Biochemical and Transcriptome-Wide Identification
of A-to-l RNA Editing Sites by ICE-Seq 331
Shunpei Okada, Masayuki Sakurai, Hiroki Ueda, and Tsutomu Suzuki
1. Introduction 332
2. Outline of the ICE-seq Protocol 334
3. Inosine Cyanoethylation with Acrylonitrile 336
4. cDNA Library Preparation and Deep Sequencing 338
5. Data Analysis 343
6. Evaluation of ICE-seq 349
Acknowledgments 350
References 350
16. Radical SAM-Mediated Methylation of Ribosomal RNA 355
Vanja Stojkovic and Danica Galonic Fujimori
1. Introduction 356
2. Mechanism of RNA Methylation by RlmN and Cfr 358
X
Contents
3. Expression of RlmN and Cfr 359
4. Purification of RlmN and Cfr 360
5. In Vitro Methylation Assays for RlmN and Cfr 362
6. In Vivo Activity Assay for RlmN and Cfr 368
7. Summary and Concluding Remarks 372
Acknowledgments 373
References 373
Author Index
Subject Index
377
399
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| series | Methods in enzymology |
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| spelling | RNA modification ed. by Chuan He 1. ed. Amsterdam [u.a.] Elesevier, Acad. Press 2015 XVIII, 409 S., [6] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 560 Modifikation Biochemie (DE-588)4307844-8 gnd rswk-swf RNS (DE-588)4076759-0 gnd rswk-swf RNS (DE-588)4076759-0 s Modifikation Biochemie (DE-588)4307844-8 s 1\p DE-604 He, Chuan Sonstige (DE-588)136032109 oth Methods in enzymology 560 (DE-604)BV000000938 560 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028227861&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
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| title | RNA modification |
| title_auth | RNA modification |
| title_exact_search | RNA modification |
| title_full | RNA modification ed. by Chuan He |
| title_fullStr | RNA modification ed. by Chuan He |
| title_full_unstemmed | RNA modification ed. by Chuan He |
| title_short | RNA modification |
| title_sort | rna modification |
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