Visualizing RNA dynamics in the cell:
Gespeichert in:
| Weitere Verfasser: | , |
|---|---|
| Format: | Elektronisch E-Book |
| Sprache: | English |
| Veröffentlicht: |
Cambridge, MA
Academic Press
2016
|
| Ausgabe: | First edition |
| Schriftenreihe: | Methods in enzymology
volume 572 |
| Schlagworte: | |
| Online-Zugang: | TUM01 UBM01 UBR01 UBT01 UBW01 UER01 Volltext Inhaltsverzeichnis |
| Beschreibung: | 1 Online-Ressource (xvi, 368 Seiten) |
| ISBN: | 9780128046807 9780128048337 |
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Datensatz im Suchindex
| _version_ | 1804176253754802176 |
|---|---|
| adam_text | Titel: Visualizing RNA dynamics in the cell
Autor: Filonov, Grigory S
Jahr: 2016
CONTENTS
Contributors xj
Preface w
1.RNA Imaging with Multiplexed Error-Robust Fluorescence
In Situ Hybridization (MERFISH) 1
J.R. Moffitt arid X. Zhuang
1. Introduction 2
2. MERFISH Overview 4
3. The Design of Oligonucleotide Probes 13
4. Probe Construction 22
5. Sample Preparation and Staining 27
6. MERFISH Imaging 31
7. MERFISH Data Analysis 39
8. Summary 48
Acknowledgments 48
References 48
2. Imaging Single mRNA Dynamics in Live Neurons and Brains 51
H.C. Moon and H.Y. Park
I. Introduction 52
2. Neuron Culture Imaging 55
3. Brain Slice Imaging 61
Acknowledgments 63
References 63
3. Monitoring of RNA Dynamics in Living Ceils Using PUM-HD
and Fluorescent Protein Reconstitution Technique 65
H. Yoshimura and T. Ozawa
I. Introduction 66
2. Principle of PUM-HD-Based RNA Probes 70
3. Development of PUM-HD-Based Probes 73
4. Microscopy Setup and Visualization of Single-Molecule RNA in Living Cells 76
5. Example of RNA Visualization by Using PUM-HD-Based RNA Probes 80
6. Conclusion 82
Acknowledgment 84
References 84
vi Contents
4. Applications of Hairpin DNA-Functionalized Gold
Nanopartides for Imaging mRNA in Living Cells 87
S.R. Jackson, A.C. Wong, A.R. Travis, I.E. Catrina, D.P. Bratu,
D.W. Wright, and A. Jayagopal
1. Introduction 88
2. Protocol for hAuNP-Guided Imaging of mRNA in Living Cells 92
3. Key Results 96
4. Conclusions 99
Acknowledgments 101
References 101
5. In Vivo RNA Visualization in Plants Using MS2 Tagging 105
EJ. Pena and M. Heinlein
1. Introduction 106
2. Plasmid Constructs: Cloning of SL-Tagged RNA and
NLS:MCP:FP into Plant Expression Vectors 111
3. Transient Expression in N. benthamiana Leaves 114
4. Imaging and Time-Lapse Image Acquisition 116
5. Summary and Perspectives 119
Acknowledg ments 119
References 119
6. TRICK: A Single-Molecule Method for Imaging the First Round
of Translation in Living Cells and Animals
J.M. Halstead, J.H. Wilbertz, F. Wippich, T. Lionnet,
A. Ephrussi, and J.A. Chao
1. Introduction
2. Design of TRICK Reporter mRNAs
3. TRICK Experiment in Mammalian Cells
4. Microscopy
5. Data Collection
6. Analysis
7. TRICK Experiment in HeLa Cells to Determine Fraction of
Untranslated mRNAs 145
8. TRICK Experiment in Drosophila 148
9, Outlook 152
Acknowledgments 153
References 153
123
124
125
128
132
138
140
Contents
vii
7. Fluctuation Analysis: Dissecting Transcriptional Kinetics
with Signal Theory 159
A. Coulon and D.R. Larson
1. Introduction 160
2. Computing and Averaging Correlation Functions 165
3. Interpretation of Correlation Functions 176
4. Common Issues and Pitfalls 182
5. Conclusion 189
References 190
8. IMAGEtags: Quantifying mRNA Transcription in Real
Time with Multiaptamer Reporters 193
J. Ray, I. Shin, M. Ilgu, L. Bendickson, V. Gupta,
G.A. Kraus, and M. Nilsen-Hamilton
1. Introduction 194
2. IMAGEtags 196
3. Visualizing Gene Expression with IMAGEtags 199
4. Measurement of IMAGEtag RNA Level by RT-qPCR 205
5. Synthesis of Ligands 207
6. Cloning Repetitive Sequences 209
7. Conclusions 211
Acknowledg ments 212
References 212
9. A Method for Expressing and Imaging Abundant,
Stable, Circular RNAs In Vivo Using tRNA Splicing 215
C.A. Schmidt, JJ. Noto, G.S. Filonov, and A.G. Matera
1. Introduction 216
2. Design and Generation of tricRNA Vectors 218
3. In Vivo Expression of tricRNAs 226
4. In-Gel Imaging of tricRNAs 229
5. Cellular Imaging of tricRNAs 233
6. Concluding Remarks 234
Acknowledgments 235
References 235
viii
Contents
10. RNA-ID, a Powerful Tool for Identifying and Characterizing
Regulatory Sequences 237
C.E. Brule, K.M. Dean, and EJ. Grayhack
1. Introduction 238
2. Features of the RNA-ID System 239
3. Applications of the RNA-ID System 241
4. Analysis of c/s-Regulatory Sequences in the RNA-ID Reporter 244
5. Verification of Regulatory Sequences 250
6. Conclusions and Extensions of the RNA-ID Reporter System 251
Acknowledgments 252
References 252
11. Fluorescent Protein-Based Quantification of Alternative
Splicing of a Target Cassette Exon in Mammalian Cells 255
N.G. Gurskaya, D.B. Staroverov, and KA Lukyanov
1. Introduction 256
2. Description of the Method 257
3. Materials 260
4. Procedure 261
5. Concluding Remarks 266
Acknowledgments 267
References 267
12. IRAS: High-Throughput Identification of Novel Alternative
Splicing Regulators 269
S. Zheng
1. Introduction 270
2. Method Design 272
3. Construction of Dual-Fluorescence Minigene Reporters 276
4. Generation of Stable Cell Clones 278
5. Library and Array Construction 280
6. Cell-Based Fligh-Throughput Screens 281
7. Data Acquisition 282
8. Background Fluorescence Correction and Normalization 285
9. Data Analysis 285
10. Validation 287
11. Limitations and Perspectives 287
References 288
Contents
ix
13. Analysis of Nonsense-Mediated mRNA Decay at
the Single-Cell Level Using Two Fluorescent Proteins 291
N.G. Gurskaya, A.P. Pereverzev, D.B. Staroverov,
N.M. Markina, and K.A. Lukyanov
1. Introduction 292
2. Description of the Method 294
3. Materials 296
4. Procedure 297
5. Further Possible Modifications of Genetic Constructs 309
6. Concluding Remarks 311
Acknowledgments 312
References 312
14. Developing Fluorogenic Riboswitches for Imaging
Metabolite Concentration Dynamics in Bacterial Cells 315
J.L. Litke, M. You. and S.R. Jaffrey
1. Introduction 316
2. Structure-Guided Design of Spinach Riboswitch Sensors 319
3. Identifying Spinach Riboswitch Sensors In Vitro 323
4. Live-Cell Imaging of Metabolites with Spinach Riboswitch Sensors 327
5. Summary and Concluding Remarks 331
Acknowledgments 332
References 332
Author Index 335
Subject Index 351
|
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| spelling | Visualizing RNA dynamics in the cell edited by Grigory S. Filonov and Samie R. Jaffrey First edition Cambridge, MA Academic Press 2016 1 Online-Ressource (xvi, 368 Seiten) txt rdacontent c rdamedia cr rdacarrier Methods in enzymology volume 572 RNS (DE-588)4076759-0 gnd rswk-swf Bildgebendes Verfahren (DE-588)4006617-4 gnd rswk-swf Methode (DE-588)4038971-6 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content RNS (DE-588)4076759-0 s Bildgebendes Verfahren (DE-588)4006617-4 s Methode (DE-588)4038971-6 s DE-604 Filonov, Grigory S. edt Jaffrey, Samie edt Methods in enzymology volume 572 (DE-604)BV021328877 572 http://www.sciencedirect.com/science/bookseries/00766879/572 Verlag URL des Erstveröffentlichers Volltext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028990281&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Visualizing RNA dynamics in the cell Methods in enzymology RNS (DE-588)4076759-0 gnd Bildgebendes Verfahren (DE-588)4006617-4 gnd Methode (DE-588)4038971-6 gnd |
| subject_GND | (DE-588)4076759-0 (DE-588)4006617-4 (DE-588)4038971-6 (DE-588)4143413-4 |
| title | Visualizing RNA dynamics in the cell |
| title_auth | Visualizing RNA dynamics in the cell |
| title_exact_search | Visualizing RNA dynamics in the cell |
| title_full | Visualizing RNA dynamics in the cell edited by Grigory S. Filonov and Samie R. Jaffrey |
| title_fullStr | Visualizing RNA dynamics in the cell edited by Grigory S. Filonov and Samie R. Jaffrey |
| title_full_unstemmed | Visualizing RNA dynamics in the cell edited by Grigory S. Filonov and Samie R. Jaffrey |
| title_short | Visualizing RNA dynamics in the cell |
| title_sort | visualizing rna dynamics in the cell |
| topic | RNS (DE-588)4076759-0 gnd Bildgebendes Verfahren (DE-588)4006617-4 gnd Methode (DE-588)4038971-6 gnd |
| topic_facet | RNS Bildgebendes Verfahren Methode Aufsatzsammlung |
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