RNA turnover in eukaryotes: analysis of specialized and quality control RNA decay pathways
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, AP
2008
|
| Series: | Methods in enzymology
449 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XLIV, 417 S., [1] Bl. Ill., graph. Darst. |
| ISBN: | 9780123745842 |
Staff View
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Record in the Search Index
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|---|---|
| adam_text | Contents
Contributors
xi
Preface
xvii
Volumes in Series
xix
Section I. Analysis of Specialized mRNA Decay Pathways
1
1.
Methods to Study No-Go mRNA Decay in Saccharomyces cerevisiae
3
Meenakshi K.
Doma
1.
Introduction
4
2.
Design and Construction of an NGD Substrate mRNA
7
3.
Methods Used to Assay Degradation Characteristics of NGD Substrates
11
4.
Conclusion
18
Acknowledgments
18
References
19
2.
Cell-Cycle Regulation of
Historie mRNA
Degradation in Mammalian
Cells: Role of Translation and Oligouridylation
23
Thomas E. Mullen, Handan Kaygun, and William F. Marzluff
1.
Introduction
24
2.
Use of the Iron Response Protein to Study the Role of Translation in
Histone mRNA Degradation
26
3.
Expression of a Dominant Negative Stem-Loop Binding Protein
33
4.
Circularization RT-PCR to Map
5
and
3
Ends of Histone mRNA
In Vivo and In Vitro and to Define mRNA Degradation Intermediates
34
5.
Oligo(dA) RT-PCR to Visualize Oligo(U) Tails on Histone mRNA following
Inhibition of
DNA
Synthesis or at the End of
S
Phase
42
6.
Summary and Conclusions
44
References
44
3.
Assays of Adenylate Uridylate-Rich Element-Mediated
mRNA Decay in Cells
47
Riza
M.
Ysla, Gerald M. Wilson, and Gary Brewer
1.
Introduction
48
2.
Reporter Gene System
50
3.
Construction of the Reporter Gene-ARE Plasmid
51
Contents
4.
Cell Culture and Transfection
53
5.
Time Course and
RNA
Isolation
55
6. Quantitäten
of mRNA Levels
57
7.
Analysis of qPCR Data for mRNA Half-Life
58
8.
Messenger
RNA
Decay Pathways
65
9.
Concluding Remarks
68
Acknowledgments
69
References
69
4.
Evaluating the Control of mRNA Decay in Fission Yeast
73
Brandon
).
Cuthbertson and Perry
).
Blackshear
1.
Introduction
74
2.
Studying mRNA Decay in Yeasts
75
3.
Systems for Studying TZF Protein-Mediated mRNA Decay
77
4.
Characterization of zfsl as a Mediator of mRNA Decay
78
5.
Use of the nmt Expression System to Evaluate zfsl-Mediated
mRNA Decay
80
6.
Northern Blot Analysis and Transcript Quantitation
86
7.
Utility of the S. pombe zfsl Model
89
Acknowledgments
92
References
92
5.
In Vivo Analysis of the Decay of Transcripts Generated
by Cytoplasm
¡c RNA
Viruses
97
Nicole L. Garneau, Carol J. Wilusz, and Jeffrey Wilusz
1.
Introduction
98
2.
Collecting
RNA
Samples
99
3.
Viral
RNA
Decay Systems
101
4.
Analysis of Viral
RNA
Decay
103
5.
Analysis of the
3
End of Viral
RNA
111
6.
Isolation of Small RNAs
117
7.
Concluding Remarks
119
Acknowledgments
120
References
120
Section II. Nonsense-Mediated mRNA Decay
(How Do You Study NMD; What Defines an NMD Target)
125
6.
Qualitative and Quantitative Assessment of the Activity of
the Yeast Nonsense-Mediated mRNA Decay Pathway
127
Feng He,
Nadia
Amrani, Marcus J. O. Johansson, and Allan
Jacobson
1.
Introduction
128
2.
Methods and Discussion
129
Contents
vii
3.
Summary
145
Acknowledgment
146
References
146
7.
Nonsense-Mediated mRNA Decay in Caenorhabdltis
elegans
149
Dasa Longman, Pablo
Arrisi,
lain
L
Johnstone,
and Javier
F. Cáceres
1.
Introduction
150
2.
Nonsense-Mediated mRNA Decay Reporter
150
3.
Protocol for a Genome-Wide RNAi-Based NMD Screen
153
4.
Protocol: Genetic Screen for Novel NMD Factors
157
5.
Validation Strategy
162
Acknowledgments
162
References
163
8.
In Vivo Analysis of Plant Nonsense-Mediated mRNA Decay
165
Koichi
Hori
and Yuichiro Watanabe
1.
Introduction
166
2.
Introducing Test and Reference Genes into Plants or Cultured
Plant Cells
166
3.
Assessing mRNA Instability by Nonsense-Mediated mRNA Decay
Inhibitor Treatment
167
4.
Comparing the Relative Stabilities of Test and Reference mRNAs
169
5.
Experiment
1
(Analysis of Endogeneous NMD Target: The Fate of
At3g63340 Splicing Variants in Arabidopsis thalmna)
170
6.
Experiment
2
(Recognition of Termination Codon Contexts as
NMD Targets in Nicotiana benthamiana)
173
References
175
9.
Studying Nonsense-Mediated mRNA Decay in Mammalian Cells
177
Daiki Matsuda, Hanae Sato, and
Lynne
E.
Maquat
1.
Introduction
178
2.
Criteria for Nonsense-Mediated mRNA Decay in Mammalian Cells
179
3.
Methods Used to Study NMD in Cultured Mammalian Cells
182
Acknowledgments
197
References
197
Contents
Section
III. Analysis of Nuclear mRNA Decay
and Non-MRNA Decay
203
10.
Estimating Nuclear mRNA Decay in Saccharomyces cerevisiae
205
Manfred
Schmid,
Mathieu
Rougemaille,
Dominico
Libri,
and
Torben Heick
Jensen
1.
Introduction
206
2.
Ways to Estimate Nuclear mRNA Decay
206
3.
Experimental System
207
4.
Protocols
214
References
218
11.
Identification and Analysis of tRNAs That Are Degraded in
Saccharomyces cerevisiae Due To Lack of Modifications
221
Irina Chernyakov, Melanie
A. Baker, Elizabeth
).
Grayhack, and
Eric M. Phizicky
1.
Introduction
222
2.
Methodology
223
3.
Identification of tRNA Species Reduced in Modification Mutants
223
4.
Analysis of the Levels of Functional tRNA In Vivo
226
5.
Characterization of the Loss of tRNA
233
6.
Conclusions
235
Acknowledgments
235
References
236
12.
Analysis of Nonfunctional Ribosomal
RNA
Decay in
Saccharomyces cerevisiae
239
Sarah E. Cole and Frederick J. LaRiviere
1.
Introduction
240
2.
Methods
241
3.
Conclusions
256
Acknowledgments
256
References
256
Section IV. Identifying Targets of an
RNA
Decay Factor
261
13.
Identifying Substrates of mRNA Decay Factors by a Combined
RNA
Interference and
DNA Microarray
Approach
263
Jürgen Wittmann
and Hans-Martin Jack
1.
Introduction
264
2.
Results
269
Contents ix
3.
Transient
hUPF2 Knockdown in HeLa
Cells
272
4. Isolation
of Total-Cell
RNA
with TRIzol
279
5.
Total-Cell
RNA
Cleanup with DNase Digestion Using Qiagen RNeasy
281
6.
Conversion of Total-Cell
RNA
to Double-Stranded cDNA
283
7.
Cleanup of Double-Stranded cDNA
285
8.
cRNA Synthesis by In Vitro Transcription
286
9.
Purification of Biotin-Labeled cRNA Transcripts Using Qiagen RNeasy
287
10.
cRNA Fragmentation
289
11.
Hybridization to
HG
-ШЗЗа
Microarrays, Washing, and
Scanning of Microarrays
290
12.
Target Confirmation and Analysis
291
Acknowledgments
292
References
293
14.
Analysis of RNA-Protein Interactions Using a Yeast
Three-Hybrid System
295
Craig R.
Stumpf,
Laura
Opperman,
and Marvin Wickens
1.
Introduction
296
2.
Principles of the Method
297
3.
Key Components: RNAs, Vectors, and Strains
298
4.
Methodology
302
5.
Analyzing Known RNA-Protein Interactions
305
6.
Three-Hybrid Screens to Identify RNA-Protein Interactions
306
7.
The Three-hybrid Screen: A General Protocol
309
8.
Other Applications of the Three-Hybrid System
312
9.
Concluding Remarks
313
Acknowledgments
313
References
313
15.
Co-lmmunoprecipitation Techniques for Assessing
RNA-Protein interactions In Vivo
317
Nicholas K. Conrad
1.
Introduction
318
2.
In Vivo Ultraviolet Cross-Unking
321
3.
Cell Mixing Experiment
327
4.
RNA Immunoprecipitation
331
5.
Discussion
336
6.
Concluding Remarks
338
Acknowledgments
339
References
339
x
Contents
Section
V.
RNAi-Mediated mRNA
Decay
343
16.
How to Define Targets for Small Guide RNAs in
RNA
Silencing:
A Biochemical Approach
345
Mikiko
С
Siomi, Kazumichi M. Nishida, and Haruhiko Siomi
1.
Introduction
346
2.
Immunopurification of Aub-piRNA Complexes from Fly
Testis Lysates
348
3.
Analyzing Protein Components Present in Immunoprecipitates
by Silver Staining and Western Blot Analysis
349
4.
Analyzing Small RNAs Present in Immunoprecipitates by
Northern Blot Analysis
349
5.
Target RNAs for Small RNA-Guided Cleavage
351
6.
In Vitro Target
RNA
Cleavage
(Slicer)
Assay
352
Acknowledgments
353
References
354
17.
Extension of Endogenous Primers as a Tool to Detect
Micro-RNA Targets
357
Sergei Vatolin and Robert J. Weil
1.
Introduction
358
2.
Reverse Transcription in Cytoplasmic Extract
359
3.
Amplification and Cloning
364
4.
Conclusion and Perspectives
368
Acknowledgments
370
References
370
18.
Examining the Influence of MicroRNAs on Translation
Efficiency and on mRNA Deadenylation and Decay
373
Ligang Wu and Joel G. Belasco
1.
Introduction
374
2.
Predicting miRNA-Responsive Elements in mRNA by
Sequence Analysis
375
3.
Using a Luciferase Reporter to Examine miRE Function
375
4.
Quantifying the Effect of a miRNA on the Translation Efficiency and
Stability of a Luciferase Reporter mRNA
380
5.
Examining the Influence of a miRNA on the Deadenylation and
Decay of
a
ß-Globin
Reporter mRNA
З84
6.
Detecting siRNA- or miRNA-Directed Endonudeolytic Cleavage
389
7.
Materials 391
Acknowledgments
392
References
392
Author Index 3g5
Subject Index
Δ11
|
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| spelling | RNA turnover in eukaryotes analysis of specialized and quality control RNA decay pathways ed. by Lynne E. Maquat ... Amsterdam [u.a.] Elsevier, AP 2008 XLIV, 417 S., [1] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 449 Eukaryotic Cells physiology Laboratory Manuals Genetic Techniques standards Laboratory Manuals Protista RNA RNA, Messenger analysis Laboratory Manuals RNA, Messenger physiology Laboratory Manuals RNS (DE-588)4076759-0 gnd rswk-swf Eukaryoten (DE-588)4070991-7 gnd rswk-swf Katabolismus (DE-588)4234092-5 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Eukaryoten (DE-588)4070991-7 s RNS (DE-588)4076759-0 s Katabolismus (DE-588)4234092-5 s DE-604 Maquat, Lynne E. Sonstige oth Methods in enzymology 449 (DE-604)BV000000938 449 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017076115&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | RNA turnover in eukaryotes analysis of specialized and quality control RNA decay pathways Methods in enzymology Eukaryotic Cells physiology Laboratory Manuals Genetic Techniques standards Laboratory Manuals Protista RNA RNA, Messenger analysis Laboratory Manuals RNA, Messenger physiology Laboratory Manuals RNS (DE-588)4076759-0 gnd Eukaryoten (DE-588)4070991-7 gnd Katabolismus (DE-588)4234092-5 gnd |
| subject_GND | (DE-588)4076759-0 (DE-588)4070991-7 (DE-588)4234092-5 (DE-588)4143413-4 |
| title | RNA turnover in eukaryotes analysis of specialized and quality control RNA decay pathways |
| title_auth | RNA turnover in eukaryotes analysis of specialized and quality control RNA decay pathways |
| title_exact_search | RNA turnover in eukaryotes analysis of specialized and quality control RNA decay pathways |
| title_full | RNA turnover in eukaryotes analysis of specialized and quality control RNA decay pathways ed. by Lynne E. Maquat ... |
| title_fullStr | RNA turnover in eukaryotes analysis of specialized and quality control RNA decay pathways ed. by Lynne E. Maquat ... |
| title_full_unstemmed | RNA turnover in eukaryotes analysis of specialized and quality control RNA decay pathways ed. by Lynne E. Maquat ... |
| title_short | RNA turnover in eukaryotes |
| title_sort | rna turnover in eukaryotes analysis of specialized and quality control rna decay pathways |
| title_sub | analysis of specialized and quality control RNA decay pathways |
| topic | Eukaryotic Cells physiology Laboratory Manuals Genetic Techniques standards Laboratory Manuals Protista RNA RNA, Messenger analysis Laboratory Manuals RNA, Messenger physiology Laboratory Manuals RNS (DE-588)4076759-0 gnd Eukaryoten (DE-588)4070991-7 gnd Katabolismus (DE-588)4234092-5 gnd |
| topic_facet | Eukaryotic Cells physiology Laboratory Manuals Genetic Techniques standards Laboratory Manuals Protista RNA RNA, Messenger analysis Laboratory Manuals RNA, Messenger physiology Laboratory Manuals RNS Eukaryoten Katabolismus Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017076115&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000000938 |
| work_keys_str_mv | AT maquatlynnee rnaturnoverineukaryotesanalysisofspecializedandqualitycontrolrnadecaypathways |