RNA editing
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2007
|
| Schriftenreihe: | Methods in enzymology
424 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
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| 245 | 1 | 0 | |a RNA editing |c ed. by Jonatha M. Gott |
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2007 | |
| 300 | |a XLV, 544 S., [5] 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 424 | |
| 650 | 4 | |a RNA editing | |
| 650 | 0 | 7 | |a Labortechnik |0 (DE-588)4123602-6 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a RNS-Edierung |0 (DE-588)4350250-7 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4143413-4 |a Aufsatzsammlung |2 gnd-content | |
| 689 | 0 | 0 | |a RNS-Edierung |0 (DE-588)4350250-7 |D s |
| 689 | 0 | 1 | |a Labortechnik |0 (DE-588)4123602-6 |D s |
| 689 | 0 | |C b |5 DE-604 | |
| 700 | 1 | |a Gott, Jonatha M. |e Sonstige |4 oth | |
| 830 | 0 | |a Methods in enzymology |v 424 |w (DE-604)BV000000938 |9 424 | |
| 856 | 4 | 2 | |m Digitalisierung UB Regensburg |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016070210&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-016070210 | |
Datensatz im Suchindex
| DE-19_call_number | 0760/8 Med.GZ 1(424 1900/WC 4355-424 1801/VK 8700.0-424 |
|---|---|
| DE-19_location | 55 29 85 |
| DE-BY-TUM_call_number | 0302 CHE 825f 03.1955 A 741 |
| DE-BY-TUM_katkey | 1609327 |
| DE-BY-TUM_location | 03 |
| DE-BY-TUM_media_number | 040030187607 |
| DE-BY-UBM_katkey | 3687422 |
| DE-BY-UBM_media_number | 41624219590017 99994612683 41620202160018 |
| _version_ | 1823053814766239744 |
| adam_text | Contents
Contributors
xiii
Preface
xix
Volumes in Series
xxi
Section I. Trypanosome
U
Insertion/Deletion
ι
1. Isolation and Compositional Analysis of Trypanosomatid Editosomes
3
Aswini K. Panigrahi,
Achim Schnaufer,
and Kenneth D. Stuart
1.
Introduction
4
2.
Isolation of Enzymatically Active Editosomes
4
3.
Identification of Protein Components
10
4.
Tandem Affinity Purification of Editosomes
15
5.
Characterization of Complexes
18
References
22
2.
Uridine Insertion/Deletion Editing Activities
25
Jason
Carnes
and Kenneth D. Stuart
1.
Introduction
26
2.
Full-Round Insertion and Deletion
27
3.
Precleaved Insertion and Deletion
35
4.
TUTase Activity
40
5.
Ligase
Activity
41
6.
Helicase
Activity
42
7.
Real-Time PCR of Editing In Vivo
43
References
52
3.
RNA
Editing Uridylyltransferases of Trypanosomatids
55
Ruslan Aphasizhev and
Inna Aphasizheva
1.
Introduction
56
2.
Purification of the
RNA
Editing TUTase
1
from Mitochondria
of Leishmania tarentolae
58
3.
Expression and Purification of
Recombinant RETi
62
4.
Isolation of the Editosome-Embedded and
Recombinant
RNA
Editing TUTase
2 64
5.
Affinity Isolation of
RET2-Contaiпίпg
Complex from T. brucei
65
vi
Contents
6. Expression
and Purification of the
Recombinant TbRET2
68
7.
Uridylyltransferase Activity Assays for the 20S
Editosome and
Recombinant RET2
69
8.
In Vitro Analysis of Protein-Protein Interactions Involving TbRET2
71
References
72
4.
Isolation of
RNA
Binding Proteins Involved in
Insertion/Deletion Editing
75
Michel
Pelletier,
Laurie K. Read, and Ruslan Aphasizhev
1.
Introduction
76
2.
Purification and Characterization of Mitochondrial
RNA
Binding Proteins
1
and
2
from Leishmania tarentolae
80
3.
Purification of the MRP1/2 Complex from Leishmania tarentolae
81
4.
Analysis of MRP1/2 Interactions in Mitochondrial Extracts
86
5.
Reconstitution
of the MRP1/2 Complex from
Recombinant
Proteins
89
6.
RNA
Binding and
RNA
Annealing Activities of the MRP1/2 Complex
91
7.
Purification of RBP16 from Procyclic Form Trypansoma brucei
94
8.
Purification of RBP16 from the Bloodstream Forms Trypansoma brucei
97
9.
Expression and Purification of
Recombinant RBP16
99
References
103
5.
RNA-Protein Interactions in Assembled Editing
Complexes in Trypanosomes
107
Jorge Cruz-Reyes
1.
Introduction
108
2.
Site-Specific Photocrosslinking Methodology to
Detect Direct Interactions of Purified Editing
Complexes with Substrates for Full-Round Editing
110
3.
Assays to Assess the Specificity of RNA-Protein
Crosslinking Interactions in Editing Complexes
117
4.
Additional Applications
121
5.
Concluding Remarks
123
References
123
6.
Strategies of Kinetoplastid Cryptogene Discovery and Analysis
127
Dmitri A. Maslov and Larry Simpson
1.
Introduction
128
2.
Cell Growth
129
3. DNA
Isolation
131
4.
Search for Cryptogenes
132
5.
Elucidation of Edited mRNA Sequences
134
6.
Search for Guide
RNA
Genes
135
References
136
Contents
vii
Section II. Physarum Insertion
Editing
141
7.
RNA
Editing in Physarum Mitochondria:
Assays and
Biochemical Approaches
143
Elaine
M.
Byrne, Linda Visomirski-Robic, Yu-Wei
Cheng,
Amy C.
Rhee, and Jonatha M.
Gott
1.
Introduction
144
2.
Experimental Systems
145
3.
RNA
Editing Assays
158
References
171
8.
Computational Approaches to Insertional
RNA
Editing
173
Ralf Bundschuh
1.
Introduction
174
2.
Overview
175
3.
Building Gene Models
176
4.
Locating Genes
178
5.
Determining Start and Stop
Codons
183
6.
Predicting Editing Site Locations
185
7.
Conclusions
193
References
194
9.
Evolution of
RNA
Editing Sites in the Mitochondrial
Small
Subunit rRNA
of the Myxomycota
197
Uma
Krishnan, Arpi Barsamian, and Dennis L. Miller
1.
Introduction
198
2.
Isolation and Amplification of Myxomycete
DNA
for Sequence Analysis
201
3.
Analysis of Mitochondrial
DNA
and cDNA Sequences
of the SSL) rRNA Core Region
204
References
218
Section III.
5
Deletion/Insertion Editing of tRNAs
221
10.
Analysis of
5 -
or
3
-Terminal tRNA Editing: Mitochondrial
5
tRNA Editing in Acanthamoeba
castellami
as the Exemplar
223
Amanda J. Lohan and Michael W. Gray
1.
Introduction
224
2.
Methods
226
3.
Concluding Remarks
240
References
240
v¡¡¡
Contents
Section
IV.
A-to-l
Editing
243
11.
Comparative Genomic and Bioinformatic Approaches for the
Identification of New Adenosine-to-lnosine Substrates
245
Jaimie Sixsmith and Robert A. Reenan
1.
Adenosine-to-lnosine
RNA
Editing
246
2.
Bioinformatics
248
3.
Comparative Genomics
249
4.
Nervous System Targets of
RNA
Editing Identified by
Comparative Genomics (Hoopengardner
et al.,
2003) 251
5.
Molecular Determinants and Guided Evolution of
Species-Specific
RNA
Editing (Reenan,
2005) 252
6.
Systematic Identification of Abundant Adenosine-to-lnosine
Editing Sites in the Human
Transcriptome (Levanon
et ai,
2004) 256
7.
Evolutionary Conserved Human Targets of Adenosine-to-lnosine
RNA
Editing (Levanon
et ai,
2005) 257
8.
Is Abundant Adenosine-to-lnosine
RNA
Editing Primate Specific?
(Eisenberg et
ai,
2005) 259
9.
A Bioinformatics Screen for Novel Adenosine-to-lnosine
RNA
Editing
Sites Reveals Recoding Editing in BC10 (Clutterluck
et ai,
2005) 260
10.
Conclusion
261
References
262
12.
Genetic Approaches to Studying Adenosine-to-lnosine
RNA
Editing
265
James
E. C
Jepson and Robert A. Reenan
1.
Introduction
266
2.
ADARs: Structure and Function
267
3.
The
Drosophila ADAR
is Required for Normal Adult
Behavior and Undergoes Transcriptional and
Posttranscriptional Regulation
269
4.
Identifying the Targets of ADAR
270
5.
The Use of Genetic Techniques to Study Adenosine-to-lnosine
Editing in
Drosophila
273
6.
Spatial and Temporal Control of
Transgenes
Using the UAS-GAL4,
Gene-Switch, and TARGET Systems
274
7.
Quantifying Adenosine-to-lnosine Editing
280
References
284
13.
A Method for Finding Sites of Selective Adenosine Deamination
289
Johan Ohlson
and Marie
Öhman
1.
Introduction
290
2.
The Choice of Organism and Tissue to Find Novel Adenosine-to-lnosine
Substrates in Mammals
291
Contents
3. Proteins
Binding to Double-Stranded
RNA
291
4.
Using Immunoprecipitation to Detect ADAR-RNA Complexes
292
5.
Using Microarray to Detect Adenosine-to-lnosine Editing Targets
294
6.
Detection of Known Site-Selectively Edited Sites Using
Specific Immunoprecipitation
294
7.
Identification of Sites of Editing within the Substrate Candidates
295
8.
ADAR2 Coimmunoprecipitation Using Mouse Brain
296
References
299
14.
Purification and Assay of ADAR Activity
301
Liam
P. Keegan, Joshua
). Rosenthal,
Loretta
M.
Roberson, and Mary A. O Connell
1.
Introduction
302
2.
Overexpression of
Recombinant
Proteins in Pichia
pastoris
302
3.
Quantification of the Efficiency of
RNA
Editing
310
References
317
15.
Large-Scale Overexpression and Purification of
ADARs from Saccharomyces cerevisiae for Biophysical
and Biochemical Studies
319
Mark R. Macbeth and Brenda L. Bass
1.
Introduction
320
2.
Methods
321
3.
Analysis of Purified hADAR2
328
4.
Future Perspectives
329
References
329
16.
Mouse Models to Elucidate the Functional
Roles of Adenosine-to-lnosine Editing
333
Elizabeth
Y. Rula
and Ronald B. Emeson
1.
Introduction
334
2.
Mammalian ADAR Enzymes
336
3.
Mammalian ADAR Substrates
338
4.
Generation of Genetically Modified Mice by
Homologous Recombination in
ES
Cells
340
5.
Classification of Transgenic Approaches
345
6.
Genetic Modification of ADAR Substrates
345
7.
Enzyme Modified Mice
353
8.
Enzyme and Substrate Modified Mice
357
References
360
Contents
17.
Probing Adenosine-to-lnosine Editing Reactions
Using RNA-Containing Nucleoside Analogs
369
Olena Maydanovych, LaHoma M. Easterwood, Tao
Cui,
Eduardo A. Véliz,
Subhash Pokharel, and
Peter A.
Beai
1.
Introduction
370
2.
Synthesis of a Substrate Analog Phosphoramidite
371
3.
General Synthetic Procedures
371
4.
Synthesis, Deprotection, and Purification of
Chemically Modified ADAR Substrate RNAs
374
5.
General Biochemical Procedures
375
6.
Evaluation of ADAR Substrate Analogs
377
7.
Synthesis of a Transition State Analog Phosphoramidite
for Mechanism-Based Trapping
379
8.
Mechanism-Based Trapping of ADAR-RNA Complexes
382
References
385
Section V. Nuclear C-to-U Editing
387
18.
Measuring Editing Activity and Identifying
Cytidine-to-Uridine mRNA Editing Factors in
Celts and Biochemical Isolates
389
Harold
С
Smith
1.
Introduction to Mammalian Cytidine-to-Uridine mRNA Editing
390
2.
Poisoned Primer Extension
392
3.
Biochemical Purification of Editing Factors
394
4.
Activity Assays
401
5.
Summary
410
References
410
19.
Mouse Models as Tools to Explore Cytidine-to-Uridine
RNA
Editing
417
Soo-Jin Cho, Valerie Blanc, and Nicholas
0.
Davidson
1.
Introduction
418
2.
apoB C-to-U
RNA
Editing
419
3.
Developmental Regulation of C-to-U
RNA
Editing
420
4.
Hormonal Regulation of C-to-U apoB
RNA
Editing
421
5.
Nutritional Modulation of C-to-U apoB
RNA
Editing
424
6.
Genetic Manipulations of Genes Involved in apoB
RNA
Editing
426
7.
Analysis of apoB
RNA
Editing
429
References
431
Contents
x¡
Section
VI.
Editing in
Plant Organelies
437
20.
RNA
Editing in
Plant Mitochondria: Assays and
Biochemical Approaches
439
Mizuki Takenaka and Axel Brennicke
1.
Introduction
440
2.
Preparation of Mitochondrial Lysates Active in
RNA
Editing
441
3.
Preparation of Templates for the
RNA
Editing Assays
445
4.
Setting up the In Vitro Test System
448
5.
The Detection System
450
6.
Crucial Parameters: Troubleshooting
454
7.
Adaptations and Assays for Common Applications
455
References
457
21.
Assay of Editing of Exogenous RNAs in
Chloroplast
Extracts of
Arabidopsis, Maize, Pea, and Tobacco
459
Michael L. Hayes and Maureen R. Hanson
1.
Introduction
460
2.
Growth Conditions for the Isolation of Intact Chloroplasts
from Tobacco, Pea, Maize, and Arabidopsis
462
3.
Isolation of Chloroplasts and Production of Editing
Competent Extracts
464
4.
Editing of Exogenous
RNA
In Vitro
466
5.
Quantification of Editing of Exogenous RNAs
474
6.
Reduction of Editing Through the Addition of Competitor RNAs
478
7.
Quantification of Editing of Endogenous RNAs
480
References
481
22.
In
Organetto
Gene Expression and
RNA
Editing Studies by
Electroporation-Mediated Transformation of Isolated
Plant Mitochondria
483
Jean-Claude Farré,
David Choury, and Alejandro Araya
1.
Introduction
484
2.
Purification of Mitochondria
486
3.
Plasmid Construction
490
4.
Electroporation-Mediated Transformation of Isolated Mitochondria
492
5.
Electrotransformation Assay and Posttranscriptional
Modifications of the Exogenous cox II
496
References
498
xii
Contents
23.
Transformation of the Plastid Genome to Study
RNA
Editing
501
Kerry
A. Lutz
and Pal Maliga
1.
Introduction
502
2.
Identification of Unique
cis
Sequences for
RNA
Editing
503
3.
Editing trans Factors
503
4.
Protocols for Construction of Transplastomic Plants
504
5.
Protocols for Testing
RNA
Editing in Tobacco Chloroplasts
513
6.
Conclusions and Future Directions
515
References
516
Author Index
519
Subject Index S37
|
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| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV022865024 |
| illustrated | Illustrated |
| indexdate | 2025-02-03T17:14:18Z |
| institution | BVB |
| isbn | 9780123739223 0123739225 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016070210 |
| oclc_num | 170033082 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-20 DE-91G DE-BY-TUM DE-12 DE-703 |
| owner_facet | DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-20 DE-91G DE-BY-TUM DE-12 DE-703 |
| physical | XLV, 544 S., [5] Bl. Ill., graph. Darst. |
| publishDate | 2007 |
| publishDateSearch | 2007 |
| publishDateSort | 2007 |
| publisher | Elsevier, Acad. Press |
| record_format | marc |
| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spellingShingle | RNA editing Methods in enzymology RNA editing Labortechnik (DE-588)4123602-6 gnd RNS-Edierung (DE-588)4350250-7 gnd |
| subject_GND | (DE-588)4123602-6 (DE-588)4350250-7 (DE-588)4143413-4 |
| title | RNA editing |
| title_auth | RNA editing |
| title_exact_search | RNA editing |
| title_full | RNA editing ed. by Jonatha M. Gott |
| title_fullStr | RNA editing ed. by Jonatha M. Gott |
| title_full_unstemmed | RNA editing ed. by Jonatha M. Gott |
| title_short | RNA editing |
| title_sort | rna editing |
| topic | RNA editing Labortechnik (DE-588)4123602-6 gnd RNS-Edierung (DE-588)4350250-7 gnd |
| topic_facet | RNA editing Labortechnik RNS-Edierung Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016070210&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000000938 |
| work_keys_str_mv | AT gottjonatham rnaediting |