RNA turnover in eukaryotes: nucleases, pathways and analysis of mRNA decay
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier
2008
|
| Schriftenreihe: | Methods in enzymology
448 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XLVIII, 607 S., [3] Bl. Ill., graph. Darst. |
| ISBN: | 9780123743787 |
Internformat
MARC
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| 245 | 1 | 0 | |a RNA turnover in eukaryotes |b nucleases, pathways and analysis of mRNA decay |c ed. by Lynne E. Maquat ... |
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier |c 2008 | |
| 300 | |a XLVIII, 607 S., [3] Bl. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Methods in enzymology |v 448 | |
| 650 | 4 | |a Eukaryotic Cells |x metabolism |v Laboratory Manuals | |
| 650 | 4 | |a Eukaryotic cells | |
| 650 | 4 | |a Genetic regulation | |
| 650 | 4 | |a Messenger RNA | |
| 650 | 4 | |a Nucleases | |
| 650 | 4 | |a RNA Precursors |v Laboratory Manuals | |
| 650 | 4 | |a RNA Stability |x physiology |v Laboratory Manuals | |
| 650 | 4 | |a RNA, Messenger |x metabolism |v Laboratory Manuals | |
| 650 | 4 | |a mRNA Cleavage and Polyadenylation Factors |v Laboratory Manuals | |
| 650 | 0 | 7 | |a RNS |0 (DE-588)4076759-0 |2 gnd |9 rswk-swf |
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| 700 | 1 | |a Maquat, Lynne E. |e Sonstige |4 oth | |
| 830 | 0 | |a Methods in enzymology |v 448 |w (DE-604)BV000000938 |9 448 | |
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| 999 | |a oai:aleph.bib-bvb.de:BVB01-017064247 | ||
Datensatz im Suchindex
| _version_ | 1804138540765806592 |
|---|---|
| adam_text | Contents
Contributors
xv
Preface
xxi
Volumes in Series
Section I. Decapping Analyses
1
1.
Analysis of mRNA Decapping
3
Shin-Wu Liu, Xinfu Jiao, Sarah Welch, and Megerditch Kiledjian
1.
Introduction
4
2.
Measuring Decapping Activities of
Recombinant
and Endogenous Dcp2
6
3.
Measuring DcpS Activity
15
4.
Migration of Cap Analogs with Various Thin-layer
Chromatography Running Buffers
17
Acknowledgment
19
References
19
2.
A Kinetic Assay to Monitor
RNA
Decapping Under
Single-Turnover Conditions
23
Brittnee
N.
Jones, Duc-Uy Quang-Dang, Yuko Oku, and John D. Gross
1.
Introduction
24
2.
Kinetic Equations
25
3.
Materials
28
4.
Kinetic Assay
30
5.
Summary
36
Acknowledgments
37
References
38
3.
Purification and Analysis of the Decapping Activator
Lsmlp-ľp-Patlp
Complex from Yeast
41
Sundaresan Tharun
1.
Introduction
42
2.
Purification of the Lsmlp^p-Patlp Complex
43
vi
Contents
3.
Analysis of
RNA
Binding by the
Lsmlp-ľp-Patlp
Complex
50
4.
Concluding Remarks
53
Acknowledgments
53
References
53
4.
Reconstitution
of
Recombinant
Human LSm Complexes for
Biochemical, Biophysical, and Cell Biological Studies
57
Bozidarka L. Zaric and Christian Kambach
1.
Introduction
58
2.
Cloning
61
3.
Protein Expression and Purification
65
4.
LSm Complex
Reconstitution
68
5.
LSm Complex Functional Assays
70
6.
Outlook
72
References
72
Section II. Polyadenylation/Deadenylation Analyses
75
5.
Regulated Deadenylation In Vitro
77
Aaron
С
Goldstrohm,
Brad A. Hook, and Marvin Wickens
1.
Introduction
78
2.
In Vitro Deadenylation Systems
80
3.
Troubleshooting
100
References
101
6.
Cell-Free Deadenylation Assays with
Drosophila
Embryo Extracts
107
Mandy
Jeske and
Elmar Wähle
1.
Introduction
107
2.
Preparation of
Drosophila
Embryo Extracts
110
3.
Preparation of Substrate
RNA
112
4.
Deadenylation Assay with
Drosophila
Embryo Extracts
113
5.
Characterization of Sequence-Dependent Deadenylation
in
Drosophila
Embryo Extracts
115
Acknowledgments
116
References
116
7.
Measuring CPEB-Mediated Cytoplasmic Polyadenylation-
Deadenylation in Xenopus laevis Oocytes and Egg Extracts
119
Jong Heon Kim and Joel D.
Richter
1.
Introduction
120
2.
Monitoring Polyadenylation of Cyclin
Bl RNA
in Xenopus laevis Oocytes
121
Contents
vii
3.
Detection of Nuclear and Cytoplasmic Polyadenylation
of X laevis Cydin Bl mRNA
126
4.
Monitoring Deadenylation and Re-adenylation
of X. laevis Cydin
Bl RNA
128
5.
Detection of Endogenous Cytoplasmic Poly(A) Polymerase Activity
130
6.
Overexpression of Exogenous mRNAs and Measuring
Polyadenylation-Deadenylation
132
7.
Preparation of X laevis Egg Extracts and Measuring
Polyadenylation-Deadenylation with Cyclin
Bl RNA
133
Acknowledgments
137
References
137
8.
The Preparation and Applications of Cytoplasmic Extracts from
Mammalian Cells for Studying Aspects of mRNA Decay
139
Kevin J. Sokoloski, Jeffrey Wilusz, and Carol J. Wilusz
1.
Introduction
140
2.
Preparation of HeLa-Cetl Cytoplasmic Extracts
142
3.
Preparation of
RNA
Substrates
148
4.
Evaluating mRNA Decay with Cytoplasmic Extracts
152
5.
Concluding Remarks
161
Acknowledgments
162
References
162
Section III. Nucleases in mRNA Decay
165
9.
In Vitro Assays of
5
to
3
Exoribonuclease Activity
167
Olivier Pellegrini, Nathalie Mathy,
Ciarán
Condon, and Lionel
Benard
1.
Introduction
168
2.
Purification ofXrnl
170
3.
In Vitro
RNA
Substrate Synthesis
171
4.
Degradation of
RNA
by XRN1 Depends on the Nature of the 5 -End
173
5.
Determining the Directionality of Decay
176
6.
Conclusions and Prospects
180
References
181
10.
Reconstitution
of
RNA
Exosomes from Human and Saccharomyces
cerevisiae: Cloning, Expression, Purification, and Activity Assays
185
Jaclyn
С
Greimann and Christopher D. Lima
1.
Introduction
186
2.
Cloning Strategies for
Recombinant
Protein Expression
190
3.
PCR and Subcloning Protocols
191
4.
PCR and Subcloning Protocols for Yeast cDNA
191
5.
PCR and Subcloning Protocols for Human cDNA
194
v¡¡¡
Contents
6. Expression
and Purification of Yeast Exosome Proteins
195
7.
Expression and Purification of Human Exosome Proteins
198
8.
Reconstitution
and Purification of Human and Yeast Exosomes
201
9.
Exoribonuclease Assays
206
10.
Comparative Exoribonuclease Assays with Different
RNA
Substrates
207
11.
Conclusions
208
Acknowledgments
208
References
209
11.
Biochemical Studies of the Mammalian Exosome
with Intact Cells
211
Geurt Schilders
and
Ger
J.
M. Pruijn
1.
Introduction
212
2.
Identifying Protein-Protein Interactions by the Mammalian
Two-Hybrid System
213
3.
Characterization of Different Exosome Subsets
by Glycerol Sedimentation
218
4.
Studying Exosome Function with RNAi
222
References
224
12.
Determining In Vivo Activity of the Yeast Cytoplasmic Exosome
227
Daneen Schaeffer, Stacie Meaux, Amanda Clark, and
Ambro
van Hoof
1.
Introduction
228
2.
Is My Favorite
RNA
Degraded and/or Processed by
the Exosome?
229
3.
Is the Cytoplasmic Exosome Active in my Mutant or
Under my Conditions?
232
References
238
13.
Approaches for Studying PMR1 Endonudease-Mediated
m
RNA
Decay
241
Yuichi Otsuka and Daniel R.
Schoenberg
1.
Introduction
242
2.
Identification of Endonuclease Cleavage Sites within mRNA
244
3.
Analysis of PMRl-Containing Complexes
251
4.
Affinity Recovery of PMRl-Containing Complexes
257
5.
Analysis of PMR1 Activity In Vivo and In Vitro
260
6.
Summary
262
Acknowledgments
262
References
262
Contents
¡χ
Section
IV. Measuring
m
RNA
Half-life In Vivo
265
14.
Methods to Determine mRNA Half-Life
in Saccharomyces cerevisiae
. 267
Jeff
Coller
1.
Introduction
268
2.
The Use of Inducible Promoters
269
3.
Measuring mRNA Decay by Use of Thermally Labile
Alíeles
of
RNA Polymerase
II
276
4.
Measuring mRNA Decay with Thiolutin
277
5.
RNA
Extractions
277
6.
Northern Blot Analysis
280
7.
Loading Controls
280
8.
Determination of mRNA Half-Lives
280
9.
Concluding Remarks
282
Acknowledgments
282
References
282
15.
mRNA Decay Analysis in
Drosophila melanogaster:
Drug-Induced
Changes in Glutathione S-Transferase D21 mRNA Stability
285
Biinyamin Akgiil and Chen-Pei D.
Tu
1.
Introduction
286
2.
Materials and Methods
287
3.
Concluding Remarks
295
Acknowledgment
296
References
296
16.
Measuring mRNA Stability During Early
Drosophila
Embryogenesis 299
Jennifer
L.
Semotok,
J.
Timothy
Westwood,
Aaron
L.
Goldman,
Ramona
L.
Cooperstock, and Howard D. Lipshitz
1.
Maternal mRNAs and Early
Drosophila
Development
300
2.
Gene-by-Gene Analysis of mRNA Decay
308
3.
Genome-Wide Analysis of mRNA Decay
318
4.
Concluding Remarks
331
Acknowledgments
331
References
332
Contents
17. Messenger
RNA
Half-Life Measurements in Mammalian Cells
335
Chyi-Ying A. Chen, Nader Ezzeddine, and Ann-Bin Shyu
1.
Introduction
336
2.
General Considerations of mRNA Half-Life Measurements
337
3.
Determining mRNA Decay Constant
338
4.
Methods for Measuring mRNA Half-Life
339
5.
Concluding Remarks
354
Acknowledgments
355
References
355
18.
Trypanosomes as a Model to Investigate mRNA
Decay Pathways
359
Stuart Archer, Rafael
Queiroz, Mhairi
Stewart, and Christine Clayton
1.
Introduction
359
2.
Genetic Manipulation in Trypanosomes: Down-Regulating
Expression of Proteins Involved in mRNA Decay
361
Acknowledgments
375
References
375
19.
Cell Type-Specific Analysis of mRNA Synthesis and
Decay In Vivo with Uracil Phosphoribosyltransferase
and 4-thiouracH
379
Michael D. Cleary
1.
Introduction
380
2.
Experimental Design Considerations
382
3.
Materials
386
4.
Methods
388
Acknowledgments
405
References
405
Section V. Defining Degradative Activities
407
20.
Analysis of Cytoplasmic mRNA Decay
in Saccharomyces cerevislae
409
Dario 0.
Passos
and Roy Parker
1.
Introduction
410
2.
Measuring mRNA Half-Life
410
3.
Determination of mRNA Decay Pathways
415
4.
Combination of the Preceding Approaches
425
References
425
Contents
x¡
21.
Transcriptome
Targets
of the Exosome Complex in Plants
429
Dmitry Belostotsky
1.
Exosome: At the Nexus of the Cellular
RNA
Transactions
429
2.
Unique Features of the Plant Exosome
432
3.
Resources for the Mutational Analyses of the Plant Exosome
434
4.
Transcriptome-wide Mapping of Targets of the Plant
Exosome Complex
436
Acknowledgments
440
References
440
22.
Sensitive Detection of
m
RNA
Decay Products by Use
of Reverse-Ligation-Mediated PCR (RL-PCR)
445
Thierry Grange
1.
Introduction
446
2.
Footprinting of RNA-Protein Interaction
450
3.
RL-PCR with Ligation of an
RNA
Linker
452
4.
Circularization RL-PCR to Analyze mRNA Decay Involving
Modification of the
5
and
З
-Ends
458
5.
Concluding Remarks
465
Acknowledgments
465
References
465
23.
Tethering Assays to Investigate Nonsense-Mediated mRNA Decay
Activating Proteins
467
Niels H.
Gehring,
Matthias W. Hentze, and Andreas E. Kulozik
1.
Introduction
468
2.
Plasmid Cloning
470
References
480
24.
Assays for Determining Poly(A) Tail Length and the Polarity
of mRNA Decay in Mammalian Cells
483
Elizabeth L. Murray and
Daniel R.
Schoenberg
1. Introduction: Poly(A) Tail Length Assays
484
2.
Introduction: Invader
RNA
Assay
492
Acknowledgments
504
References
504
xü
Contents
Section VI. Cell Biology of
RNA
Decay
(i.e., Translational Repression/P Bodies)
505
25.
Analyzing P-bodies in Saccharomyces cerevisiae
507
Tracy Nissan and Roy Parker
1.
Introduction
508
2.
Determining Whether a Specific Protein Can Accumulate in P-Bodies
508
3.
Monitoring Messenger
RNA
in P-Bodies
514
4.
Determining Whether a Mutation or Perturbation Affects P-Body
Size and Number
515
5.
Quantification of P-Body Size and Number
518
Acknowledgments
519
References
519
26.
Real-Time
and Quantitative Imaging of Mammalian Stress
Granules and Processing Bodies
521
Nancy Kedersha, Sarah Tisdale, Tyler Hickman, and Paul Anderson
1.
Introduction
522
2.
Experimental Rationale
524
3.
Experimental Considerations
524
4.
Selection Criteria
527
5.
Transfection
528
6.
Properties of Representative Stable Lines
533
7.
Environmental Control
541
8.
Microscope Hardware: Widefield vs Confocal
543
9.
Useful Microscopy Internet Resources
547
10.
Sample Protocols
547
11.
Conclusions
551
References
551
27.
Cell Biology of mRNA Decay
553
David
Grünwald,
Robert H. Singer, and Kevin Czaplinski
1.
Introduction
554
2.
FISH Probe Design
556
3.
Hybridization
557
4.
Image Acquisition
557
5.
FISH Protocol
558
6.
Colabeling Protein with IF and
RNA
with FISH
560
7.
IF-FISH Protocol
561
8.
Following mRNA in Living Cells
562
9.
Live Single-Molecule Detection
563
Contents
x¡¡¡
10. Single mRNA Data
Analysis; What You Can Observe
564
11.
How Do You Know That You See Single Molecules?
566
12.
The Secret to Getting Good Data: More Photons, Less Noise
568
13.
Setting Up a Microscope for Single Molecule Detection
569
14.
Conclusion
571
Acknowledgments
571
References
575
Author Index
579
Subject Index
597
|
| any_adam_object | 1 |
| building | Verbundindex |
| bvnumber | BV035258695 |
| callnumber-first | Q - Science |
| callnumber-label | QP623 |
| callnumber-raw | QP623.5.M47 |
| callnumber-search | QP623.5.M47 |
| callnumber-sort | QP 3623.5 M47 |
| callnumber-subject | QP - Physiology |
| classification_rvk | WC 4355 |
| ctrlnum | (OCoLC)304074738 (DE-599)BVBBV035258695 |
| dewey-full | 572.88 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.88 |
| dewey-search | 572.88 |
| dewey-sort | 3572.88 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Book |
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| illustrated | Illustrated |
| indexdate | 2024-07-09T21:29:49Z |
| institution | BVB |
| isbn | 9780123743787 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-017064247 |
| oclc_num | 304074738 |
| open_access_boolean | |
| owner | DE-12 DE-20 DE-19 DE-BY-UBM DE-355 DE-BY-UBR DE-91G DE-BY-TUM |
| owner_facet | DE-12 DE-20 DE-19 DE-BY-UBM DE-355 DE-BY-UBR DE-91G DE-BY-TUM |
| physical | XLVIII, 607 S., [3] Bl. Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | Elsevier |
| record_format | marc |
| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | RNA turnover in eukaryotes nucleases, pathways and analysis of mRNA decay ed. by Lynne E. Maquat ... Amsterdam [u.a.] Elsevier 2008 XLVIII, 607 S., [3] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 448 Eukaryotic Cells metabolism Laboratory Manuals Eukaryotic cells Genetic regulation Messenger RNA Nucleases RNA Precursors Laboratory Manuals RNA Stability physiology Laboratory Manuals RNA, Messenger metabolism Laboratory Manuals mRNA Cleavage and Polyadenylation Factors 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 448 (DE-604)BV000000938 448 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017064247&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | RNA turnover in eukaryotes nucleases, pathways and analysis of mRNA decay Methods in enzymology Eukaryotic Cells metabolism Laboratory Manuals Eukaryotic cells Genetic regulation Messenger RNA Nucleases RNA Precursors Laboratory Manuals RNA Stability physiology Laboratory Manuals RNA, Messenger metabolism Laboratory Manuals mRNA Cleavage and Polyadenylation Factors 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 nucleases, pathways and analysis of mRNA decay |
| title_auth | RNA turnover in eukaryotes nucleases, pathways and analysis of mRNA decay |
| title_exact_search | RNA turnover in eukaryotes nucleases, pathways and analysis of mRNA decay |
| title_full | RNA turnover in eukaryotes nucleases, pathways and analysis of mRNA decay ed. by Lynne E. Maquat ... |
| title_fullStr | RNA turnover in eukaryotes nucleases, pathways and analysis of mRNA decay ed. by Lynne E. Maquat ... |
| title_full_unstemmed | RNA turnover in eukaryotes nucleases, pathways and analysis of mRNA decay ed. by Lynne E. Maquat ... |
| title_short | RNA turnover in eukaryotes |
| title_sort | rna turnover in eukaryotes nucleases pathways and analysis of mrna decay |
| title_sub | nucleases, pathways and analysis of mRNA decay |
| topic | Eukaryotic Cells metabolism Laboratory Manuals Eukaryotic cells Genetic regulation Messenger RNA Nucleases RNA Precursors Laboratory Manuals RNA Stability physiology Laboratory Manuals RNA, Messenger metabolism Laboratory Manuals mRNA Cleavage and Polyadenylation Factors Laboratory Manuals RNS (DE-588)4076759-0 gnd Eukaryoten (DE-588)4070991-7 gnd Katabolismus (DE-588)4234092-5 gnd |
| topic_facet | Eukaryotic Cells metabolism Laboratory Manuals Eukaryotic cells Genetic regulation Messenger RNA Nucleases RNA Precursors Laboratory Manuals RNA Stability physiology Laboratory Manuals RNA, Messenger metabolism Laboratory Manuals mRNA Cleavage and Polyadenylation Factors Laboratory Manuals RNS Eukaryoten Katabolismus Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017064247&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000000938 |
| work_keys_str_mv | AT maquatlynnee rnaturnoverineukaryotesnucleasespathwaysandanalysisofmrnadecay |