RNA and DNA editing: molecular mechanisms and their integration into biological systems
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Hoboken, N.J.
Wiley-Interscience
2008
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Includes bibliographical references and index |
| Beschreibung: | XXIII, 426 S. Ill., graph. Darst. |
| ISBN: | 9780470109915 |
Internformat
MARC
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| 010 | |a 2007039289 | ||
| 020 | |a 9780470109915 |c cloth |9 978-0-470-10991-5 | ||
| 035 | |a (OCoLC)173469796 | ||
| 035 | |a (DE-599)BVBBV023303865 | ||
| 040 | |a DE-604 |b ger |e aacr | ||
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| 044 | |a xxu |c US | ||
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| 084 | |a WG 1800 |0 (DE-625)148501: |2 rvk | ||
| 245 | 1 | 0 | |a RNA and DNA editing |b molecular mechanisms and their integration into biological systems |c ed. by Harold C. Smith |
| 264 | 1 | |a Hoboken, N.J. |b Wiley-Interscience |c 2008 | |
| 300 | |a XXIII, 426 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Includes bibliographical references and index | ||
| 650 | 4 | |a Base Sequence | |
| 650 | 4 | |a DNA | |
| 650 | 4 | |a Genetic transcription | |
| 650 | 4 | |a Genomics | |
| 650 | 4 | |a Nucleotide sequence | |
| 650 | 4 | |a RNA Editing | |
| 650 | 4 | |a RNA editing | |
| 650 | 4 | |a Transcription, Genetic | |
| 650 | 0 | 7 | |a Transkription |g Genetik |0 (DE-588)4185906-6 |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 | |5 DE-604 | |
| 689 | 1 | 0 | |a Transkription |g Genetik |0 (DE-588)4185906-6 |D s |
| 689 | 1 | |C b |5 DE-604 | |
| 700 | 1 | |a Smith, Harold C. |e Sonstige |4 oth | |
| 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=016488270&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-016488270 | ||
Datensatz im Suchindex
| _version_ | 1804137633928970240 |
|---|---|
| adam_text | CONTENTS
PREFACE
XV
ACKNOWLEDGMENTS
xix
CONTRIBUTORS
xxi
part
t
DIVERSIFICATION OF THE PROTEOME THROUGH
RNA
AND
DNA
EDITING
CHAPTER
1
DIVERSIFYING
ΕΧΟΝ
CODE THROUGH A-TO-I
RNA
EDITING
_________3
1.1
Introduction and Background
3
1.1.1
Initial Discovery and Context of A-to-I
RNA
Editing and ADARs
4
1.1.2
Important Cases of Recoding by A-to-I Modification
in Pre-mRNA
5
1.1.3
Cis-
Acting Features for A-to-I Editing
14
1.1.4
Properties of the A-to-I Editing Machinery
15
1.2
Main Questions in the Field and Approaches
17
1.2.1
Biochemical Versus Computational Approaches
17
1.2.2
Editing of miRNA Sequences
21
1.3
Future Directions: Evolution of Editing Sites and Machinery
23
References
24
CHAPTER
2
ANTIBODY GENE DIVERSIFICATION BY AID-CATALYZED
__________DNA
EDITING
________________________________________________31.
2.1
Introduction
31
2.2
Before AID
32
2.2.1
Without
DNA
(Darkness) and with
DNA
(Light)
32
2.2.2
Prominent Early Models for Antibody Diversification
32
2.2.3
How Protein Sequencing Technology Enabled an Understanding
of Antibody Diversity
34
2.2.4
Somatic
DNA
Rearrangements Underpin V(D)J Joining
and Create the Primary Antibody Repertoire
37
2.2.5
Additional Antibody Diversity by Somatic Hypermutation
(and Gene Conversion in Some Animals)
40
2.2.6
Altering Antibody Function by Class Switch Recombination
(Isotype
Switching)
40
2.3
After AID
41
2.3.1
A Novel Deaminase Is Required for CSR, SHM, and IGC
41
VI
CONTENTS
2.3.2
AID Is
a
DNA
Cytosine Deaminase that Directly Triggers Antibody
Diversification
43
2.3.3
The Importance of Uracil Bases in
DNA In
Vivo
45
2.3.4
Processing of AID-induced Lesions: The Molecular Mechanism
of Somatic-Hypermutation
48
2.3.5
Processing of AID-induced Lesions: The Molecular Mechanism of
Immunoglobulin Gene Conversion
49
2.3.6
Processing of AID-induced Lesions: The Molecular Mechanism of
Class Switch Recombination
50
2.4
Hot Areas and Speculations
53
2.4.1
Immunodeficiency Syndromes Caused by Defects in
AID-Mediated Ig Gene
Diversification
53
2.4.2
Regulating the
DNA Mutator
Activity of AID
54
2.4.3
Misregulation of AID and Cancer
57
2.4.4
AID Is But One Member of a Much Larger Family of
Polynucleotide Deaminases
58
2.5
Conclusions
60
Acknowledgments
60
References
61
CHAPTER
з
PROTEIN-PROTEIN AND RNA-PROTEIN INTERACTIONS
___________
IN
U
-INSERTION/DELETION
RNA
EDITING COMPLEXES
____________71
3.1
A Bi/.arre Phenomenon and its
Raison D
étre
71
3.2
The Catalytic Mechanism and Machinery
73
3.3
Extent of
U
-Insertion/Deletion
RNA
Editing in Trypanosoma
and Leishmania Species
75
3.4
Functional Studies of Editing Complex Subunits
76
3.4.1
RENI,
REN2, and MP67. Endonuclease Homologs
80
3.4.2
REX1 and REX2. Exonuclease Homologs
83
3.4.3
RET2. TUTasc
85
3.4.4
RELI
and REL2.
Ligase
Homologs
85
3.4.5
MP81, MP63, MP42, MP46, MP44, MP24, MP18.
Structural Components
87
3.5
RNA-Protein Interactions: Isolated Subunits and Assembled
Editing Complexes
92
3.5.1
MP42
92
3.5.2
MP24
93
3.5.3
RNA-Protein Interactions in Assembled Editing Complexes
93
3.6
Concluding Remarks
96
Acknowledgments
96
References
96
CHAPTER
4
MACHINERY OF
RNA
EDITING IN
ΡΙΛΝΤ
ORGANELLES
99
4.1
Introduction
99
4.2
Mechanism of Target Recognition
100
4.3
PPR
Protein is a Trans-Factor in Plastids
101
4.4
How Can the Model Be Generalized to Plant
RNA
Editing?
104
4.5
Can Closely Located Editing Sites Share
a íraraí-Factor?
105
CONTENTS
VII
4.6
Is a Trans-Factor Specific to a Single Cis-Element?
106
4.7
Mechanism Determining the Efficiency of
RNA
Editing
107
4.8
Co-Evolution of Tram-Factors and Editing Sites
109
4.9
What is an Editing Enzyme?
110
4.10
A Model of Editing Machinery in Plastids
112
4.11
Future Directions
114
Acknowledgments
114
References
114
part
и
FUNCTIONAL COORDINATION OF
RNA
EDITING
WITH OTHER CELLULAR MECHANISMS
CHAPTER
5
TRANSFER
RNA
EDITING ENZYMES; AT THE CROSSROADS
__________
OF AFFINITY AND SPECIFICITY
________________________________123
5.1
Introduction: Structural Versus Functional tRNA Editing
123
5.2
Transfer
RNA
Editing for Structure
124
5.2.1
C-to-U Editing of the tRNA Backbone
124
5.2.2
A-to-I Editing and Modification at Position
37
and
57
of tRNAs
126
5.3
Transfer
RNA
Editing for Function
127
5.3.1
The Lysidine Story
127
5.3.2
Nucleotide Additions at the Ends of tRNAs
130
5.3.3
C-to-U Editing in Marsupials and Trypanosomatids
133
5.3.4
A-to-I Editing of tRNAs in Yeast and Bacteria
137
5.3.5
Double Editing in Trypanosomatids
139
5.4
The Transfer
RNA
Editing Enzymes of Trypanosomatids:
A Special Case of Catalytic Flexibility
140
5.5
Complex Formation by Transfer
RNA
Editing Enzymes:
A Model for the Regulation of Editing Activity
141
5.6
Concluding Remarks: Evolution of Transfer
RNA
Editing
Deaminases: Affinity Versus Specificity
142
References
143
CHAPTER
6
A-TO-I EDITING AS A CO-TRANSCRIPTIONAL
RNA
__________
PROCESSING EVENT
__________________________________________146
6.1
Introduction
146
6.1.1
Overview of Co-transcriptional Pre-mRNA Processing
147
6.1.2
Localization of the ADAR Proteins
148
6.1.3
A-to-I Editing as a Pre-mRNA Processing Event
149
6.2
Main Questions in the Field and Approaches
149
6.2.1
Why Are Edited Sites Often Situated Close to
Exon/bitron
Border?
149
6.2.2
The Potential of A-to-I Editing in Changing the
Transcriptome
151
6.2.3
RNA
Editing, the Influence on Pre-mRNA Splicing and Vice Versa
152
6.3
Can Editing Influence the Fate of a Messenger
RNA
in Other Ways?
156
6.3.1
Editing and Its Potential Effect on
RNA
Export
156
6.3.2
Editing as a Modulator of
RNA
Stability
156
6.3.3
Editing and Its Influence on Polyadenylarion
157
6.4
Prospectives
for Future Research
158
References
159
VIII CONTENTS
CHAPTER
7
STUDYING AND WORKING WITH RIBONUCLEOPROTEINS
__________
THAT CATALYZE H/ACA GUIDED
RNA
MODIFICATION
_____________162
7.1
Introduction
162
7.2
Discovery of Complex (RNA-guided) Pseudouridine Synthases
164
7.3
Approaches and Challenges
164
7.4
RNP
Reconstitution
166
7.5
Lessons from Archaeal H/ACA RNPs
167
7.6
Biogenesis ofEukaryotic H/ACA RNPs
168
7.7
Debate on Dyskeratosis
Congenita
168
7.8
Importance and Future of H/ACA RNPs
169
Acknowledgments
170
References
171
CHAPTER
8
FUNCTIONAL ROLES OF SPLICEOSOMAL snRNA
__________
MODIFICATIONS IN PRE-mRNA SPLICING
________________________175
8.1
Introduction
175
8.2
Modified Nucleotides in Spliceosomal snRNAs
176
8.3
Functional Analysis of Spliceosomal snRNA Modifications
179
8.4
Modified Nucleotides of U2 snRNA are Important
for
Ргє
-mRNA
Splicing
180
8.5
U2 Modifications Contribute to snRNP Biogenesis
and Spliceosome Assembly
182
8.6
Genetic Analysis of
Ш
Modification in Yeast
183
8.7
Cytotoxicity Associated with 5FU Treatment is a Result of Inhibition
on Pseudouridy
lation
and Splicing
184
8.8
Biophysical Analysis of U2 snRNA Modification
185
8.9
Concluding Remarks
186
References
186
CHAPTER
9
A ROLE FOR A-TO-I EDITING IN GENE SILENCING
________________190
9.1
Expression of Double-Stranded
RNA
in Cells
190
9.2
The Activity of ADAR in the Nucleus
191
9.3
Alternative Fates of Edited RNAs in the Nucleus
192
9.4
A Possible Connection Between
RNA
Editing and Gene Silencing
193
9.4.1
Heterochromatin
193
9.4.2
RNAi-Directed Heterochromatin Formation
194
9.4.3
Connections Between RNAi and dsRNA Editing
196
9.4.4
Vigilin
196
9A5 Recognition of
RNA
by Vigilins
197
9.4.6
The Vigilin Complex
198
9.5
A Model for the Nuclear Function of Vigilin
199
References
200
CHAPTER
10
BIOWGICALIMPUCATIONS AND BROADER-RANGE FUNCTIONS
FORAPOBEC-l ANDAPOBEC-l COMPIlSMENTAimN
___________
FACTOR (ACF)
_____________________________________________
10.1
Overview
203
CONTENTS
IX
10.2
Background to Our Current Understanding of C-to-U Editing of ApoB mRNA:
Canonical Functions for Apobec-l andACF
204
10.2.1
Role of
Cis-
Acting Elements
204
10.2.2
Identification and Characterization of Trans-Acting Factors
206
10.3
Current Understanding of Apobec-l and ACF: Structure-Function
and Genetic Regulation
209
10.3.1
Apobec-l: Structure-Function Relationships
209
10.3.2
Functions of Apobec-l Beyond apoB mRNA Editing
210
10.3.3
Apobec-l: Genetic Regulation and Gain-and Loss-of-Function
212
10.3.4
ACF: Structure-Function Relationships
214
10.3.5
Intersections of Apobec-l and ACF Regulation in the Modulation
of C-to-U
RNA
Editing
216
10.4
Implications and Broad-Range Function for Apobec-l and ACF:
Future Directions and Overarching Questions
218
10.4.1
Apobec-l
218
10.4.2
ACF
220
10.5
Conclusions
224
Acknowledgments
224
References
224
CHAPTER
1
ANTIVIRAL FUNCTION OF APOBEC3 CYTIDINE DEAMINASES
231
11.1
Explanation of
Vif Phenotype
Uncovers a Unique Innate Resistance to
HIV-1 Infection
231
11.2
Antiviral Functionality of the APOBEC3 Family of Proteins
232
11.2.1
Mechanism of Action
232
11.2.2
APOBEC3 Proteins and the Prevention of Zoonosis
235
11.2.3
In Vivo Correlations Between APOBEC3 Expression and Disease Course
236
11.3
The Battle for Control: Viral Suppression of the APOBEC3 Proteins
237
11.3.1
The Hijacking of the Proteasomal Degradation Pathways
237
11.3.2
Virion Exclusion of the APOBECs via a Viral-Dependent Mechanism
238
11.4
Cellular Function and Regulation of the APOBEC3 Family
238
11.4.1
Guardians of the Genome:
АРОВЕСЗ
-Međiated
Suppression
of Cellular Retroelements
238
11.4.2
Subcellular Localization (Sequestration)
239
11.4.3
Control of the Expression of the APOBEC3 Family is Exerted
Transcriptionally
240
11.5
Research Questions and the Hope of Therapeutic Manipulation of the
APOBEC3 Family
243
11.5.1
The Alternative Function
244
11.5.2
Protein Partitiomng/Subcellular Localization
245
11.5.3
Protein Cofactors and Posttranslational Modifications
245
11.5.4
Therapeutic Potential
246
References
247
PARTHt PMBicmm structures
CHAPTER
12
A-TO-I EDITING OF Aim REPFATS
______________________________257
12.1
Background
257
12.1.1
Indirect Evidence for Abundant A-to-I Editing
257
X
CONTENTS
12.1.2
Early Screens for A-to-I Editing Targets
258
12.1.3
The
Alu
Repeats
259
12.2
Computational Detection of A-to-I Editing
260
12.2.1
Sifting through
db EST
260
12.2.2
Clusters of Mismatches in RNAs
262
12.2.3
Numbers of Editing Sites Detected
265
12.2.4
Characterization of the Edited Transcripts
265
12.2.5
Looking for Conserved Polymorphism Sites
267
12.2.6
Additional Potential Targets for Abundant A-to-I Editing
267
12.3
Editing in Other Organisms
268
12.3.1
Uniqueness of the
Alu
Repeat
269
12.3.2
Predicting Editing Sites from Genomic Data
270
12.4
Biological Role of
Afe
Editing
272
12.4.1
Possible Regulatory Roles
272
12.4.2
Alu
Editing and miRNA
272
12.4.3
Alternative Splicing and
Alu
Editing
273
12.5
Concluding Remarks
275
References
276
CHAPTER
13
RNA
EDITING IN DINOFLAGELLATES AND ITS IMPLICATIONS
FOR THE EVOLUTIONARY HISTORY OF THE
__________
EDITING MACHINERY
________________________________________280
13.1
Introduction
280
13.2
Inferred
RNA
Editing in Dinoflagellates
283
13.2.1
cob and
««7
mRNA
283
13.2.2
Chloroplast Transcripts
288
13.3
Biochemical Characteristics of Editing
289
13.3.1
Unusually Diverse Types of Editing
289
13.3.2
Varying Editing Density and Discrete Distribution of Editing Events
in Coding Sequences
293
13.3.3
Markedly Nonrandom Distribution in the Type of Codon Edited
and in the Position of the Editing Site Within
Codons
294
13.4
Consequences of Editing
297
13.5
Phylogenetic Trend
301
13.6
Implications for the Origin and Evolution of the
RNA
Editing Machinery
304
Acknowledgment
306
References
306
part
iv
STRUCTURAL APPROACHES
CHAPTER
14
THE BOX C/D RNPs: EVOLUTIONARILY ANCIENT
__________
NUCLEOTIDE MODIFICATION COMPLEXES
_____________________313
14.1
Introduction
313
14.2
Diversity of Box
C/D RNA
Populations
314
14.2.1
Box
C/D RNA
Nomenclature
314
14.2.2
Box
C/D RNA
Structure
315
CONTENTS
XI
14.2.3
Diversity of Box
C/D RNA
Populations
316
14.2.4
Box
C/D RNA
Identification
316
14.3
Box
C/D RNA
Functions and Target RNAs
319
14.3.1
Folding and Cleavage of Pre-rRXA
319
14.3.2
^-O-Methylation of Diverse
RNA
Targets
319
14.3.3
Additional Roles and Targets for Box CD RNAs
320
14.4
Box C/D RNP Structure and Nucleotide Methylation Function
321
14.4.1
Eukaryotic Box C/D Core Proteins and snoRNP Structure
321
14.4.2
Archaeal Box C/D Core Proteins and In Vitro sRNP
Assembly
322
14.4.3
Emerging Core Protein and RNP Crystal Structures
322
14.4.4
Investigating Methylation Function Using In Vitro Assembled
Archaeal Box C/D sRNP
323
14.5
Box C/D RNP Biogenesis
323
14.5.1
Genomic Organization of Eukaryotic Box C/D snoRNA Genes
323
14.5.2
Independently Transcribed and Intronic Eukaryotic Box C/D
snoRNA Genes
324
14.5.3
Archaeal Box C/D sRNA Genes
324
14.5.4
Transcription and Processing of Independently Transcribed
Box C/D snoRNAs
325
14.5.5
Transcription and Processing of Intronic Box C/D
snoRNAs
326
14.5.6
Box C/D snoRNP Transport
327
14.6
Future Directions and Experimental Challenges
327
14.6.1
Box C/D
RNA
Diversity, Targets, and Functions
327
14.6.2
Box C/D RNP Structure and Methylation Function
328
14.6.3
Box C/D RNP Biogenesis
330
Acknowledgments
331
References
331
CHAPTER
15
STRUCTURAL FEATURES OF THE ADAS. FAMILY
___________
OF ENZYMES AND THEIR SUBSTRATES
__________________ 340
15.1
ADAR Enzymes
340
15.2
Overview and Functions of ADARs
341
15.2.1
Double-Stranded
RNA
Binding Domains (dsRBDs)
344
15.2.2
Xenopus laevis XIrbpa
345
15.2.3
ADAR2 dsRBDl and dsRBD2
346
15.2.4
Deaminase Domain
346
15.2.5
Za
and
Zß
Domains
347
15.2.6
Za
Structure
349
15.2.7 Zß
Structure
351
15.2.8
Structural Comparison of
Za
and
Zß 354
15.3
Conclusions
354
15.4
Substrates
355
15.4.1
Overview and General Features
355
15.5
Double-Stranded
RNA
Targets and Structural Features
355
15.5.1
Site-Selective A-to-I Editing
355
15.5.2
Structural Features of Site-Selective A-to-I Editing
358
15.5.3
Promiscuous Editing
359
XII CONTENTS
15.6
Single-stranded
RNA
Targets 361
15.7
Z-DNA and Z-RNA Targets
361
15.8
Future Directions
362
References
362
CHAPTER
16
CHEMISTRY, PHYLOGENY, AND THREE-DIMENSIONAL
___________
STRUCTURE OF THE APOBEC PROTEIN FAMILY
_________________369
16.1
Introduction to Nucleic Acid Deamination with Implications
for Biological Activity
369
16.2
The Chemistry of the Zinc-Dependent Deaminase
Amino
Acid
Signature Motif
370
16.3
The ZDD Signature Motif Implies a Specific Three-Dimensional
Arrangement of
Amino
Acids
371
16.4
Rationale for a Combined Structural and Phylogenetic Approach to
Understand APOBEC Evolution
373
16.4.1
The Starting Point for Structural and Phylogenetic Analyses of
APOBEC Family Members
375
16.4.2
The
CDA
Superfamily: Overview of Conserved Fold Topology in the
Core and Common Variations
379
16.4.3
Comparison of the Common
CDA
Superfamily Core Reveals
Broad Peripheral Diversification
381
16.5
Modes of Oligomerization
382
16.5.1
Free Nucleotide Cytidine Deaminases
(CDA):
Strand
ß5 Antiparallel
to Strand
Џ
382
16.5.2
Cytosine Deaminase, Guanine Deaminase, and TadA:
Strand
ß5
Parallel to
Џ
382
16.5.3
Deoxcytidylate Deaminases (T4,
N.
e) and APOBEC2:
Strand
ß5
Parallel to
ß4 383
16.5.4
Multidomain Enzymes RibG and ADAR2 of the
CDA
Superfamily:
Strand
ß5
Parallel to
ß4 387
16.6
Modes of Substrate Interaction
388
16.6.1
Tetrameric fnCDAs Favor Flexible Flaps:
RNA
Editing and the
Case of Cddl from Yeast
390
16.6.2
A Topological Transformation Obstructs Active Site Accessibility
in Dimerie Deaminases that Bind Bases
391
16.6.3
Substrate Selection by Polynucleotide Editing Enzymes
Remains Elusive
391
16.7
The APOBEC Family: Insights into a Structurally Underrepresented Family
392
16.7.1
Activation-Induced Deaminase (AID)
—
an Ancient Enzyme
with Essential Roles in Adaptive Immunity
395
16.7.2
APOBEC2
—
A Divergent Ancestral Protein of Unknown Function
396
16.7.3
APOBECl—The Historical Archetype of C-to-U Editing Enzymes
397
16.7.4
APOBEC4
—
Pushing the Envelope of APOBEC Boundaries
399
16.8
APOBEC3—
Radiative Expansion of Proteins Involved in Viral Defense
400
16.8.1
Mechanisms of Primate-Specific Expansion of the APOBEC3 Proteins
402
16.8.2
Alternative Methods to Obtain Structure: The Molecular Envelope
of
АРОВЕСЗО
by Small-Angle
Х
-Ray Scattering
405
16.8.3
Characterization of Structural Changes in
АРОВЕСЗО
Morphology
in the Presence of
RNA
406
CONTENTS XIII
16.8.4 Positive
Selection Exerted on the APOBEC3 Family
408
16.9
Conclusions and Future Prospects
410
References
411
INDEX
421
|
| adam_txt |
CONTENTS
PREFACE
XV
ACKNOWLEDGMENTS
xix
CONTRIBUTORS
xxi
part
t
DIVERSIFICATION OF THE PROTEOME THROUGH
RNA
AND
DNA
EDITING
CHAPTER
1
DIVERSIFYING
ΕΧΟΝ
CODE THROUGH A-TO-I
RNA
EDITING
_3
1.1
Introduction and Background
3
1.1.1
Initial Discovery and Context of A-to-I
RNA
Editing and ADARs
4
1.1.2
Important Cases of Recoding by A-to-I Modification
in Pre-mRNA
5
1.1.3
Cis-
Acting Features for A-to-I Editing
14
1.1.4
Properties of the A-to-I Editing Machinery
15
1.2
Main Questions in the Field and Approaches
17
1.2.1
Biochemical Versus Computational Approaches
17
1.2.2
Editing of miRNA Sequences
21
1.3
Future Directions: Evolution of Editing Sites and Machinery
23
References
24
CHAPTER
2
ANTIBODY GENE DIVERSIFICATION BY AID-CATALYZED
_DNA
EDITING
_31.
2.1
Introduction
31
2.2
Before AID
32
2.2.1
Without
DNA
(Darkness) and with
DNA
(Light)
32
2.2.2
Prominent Early Models for Antibody Diversification
32
2.2.3
How Protein Sequencing Technology Enabled an Understanding
of Antibody Diversity
34
2.2.4
Somatic
DNA
Rearrangements Underpin V(D)J Joining
and Create the Primary Antibody Repertoire
37
2.2.5
Additional Antibody Diversity by Somatic Hypermutation
(and Gene Conversion in Some Animals)
40
2.2.6
Altering Antibody Function by Class Switch Recombination
(Isotype
Switching)
40
2.3
After AID
41
2.3.1
A Novel Deaminase Is Required for CSR, SHM, and IGC
41
VI
CONTENTS
2.3.2
AID Is
a
DNA
Cytosine Deaminase that Directly Triggers Antibody
Diversification
43
2.3.3
The Importance of Uracil Bases in
DNA In
Vivo
45
2.3.4
Processing of AID-induced Lesions: The Molecular Mechanism
of Somatic-Hypermutation
48
2.3.5
Processing of AID-induced Lesions: The Molecular Mechanism of
Immunoglobulin Gene Conversion
49
2.3.6
Processing of AID-induced Lesions: The Molecular Mechanism of
Class Switch Recombination
50
2.4
Hot Areas and Speculations
53
2.4.1
Immunodeficiency Syndromes Caused by Defects in
AID-Mediated Ig Gene
Diversification
53
2.4.2
Regulating the
DNA Mutator
Activity of AID
54
2.4.3
Misregulation of AID and Cancer
57
2.4.4
AID Is But One Member of a Much Larger Family of
Polynucleotide Deaminases
58
2.5
Conclusions
60
Acknowledgments
60
References
61
CHAPTER
з
PROTEIN-PROTEIN AND RNA-PROTEIN INTERACTIONS
_
IN
U
-INSERTION/DELETION
RNA
EDITING COMPLEXES
_71
3.1
A Bi/.arre Phenomenon and its
Raison D
'étre
71
3.2
The Catalytic Mechanism and Machinery
73
3.3
Extent of
U
-Insertion/Deletion
RNA
Editing in Trypanosoma
and Leishmania Species
75
3.4
Functional Studies of Editing Complex Subunits
76
3.4.1
RENI,
REN2, and MP67. Endonuclease Homologs
80
3.4.2
REX1 and REX2. Exonuclease Homologs
83
3.4.3
RET2. TUTasc
85
3.4.4
RELI
and REL2.
Ligase
Homologs
85
3.4.5
MP81, MP63, MP42, MP46, MP44, MP24, MP18.
Structural Components
87
3.5
RNA-Protein Interactions: Isolated Subunits and Assembled
Editing Complexes
92
3.5.1
MP42
92
3.5.2
MP24
93
3.5.3
RNA-Protein Interactions in Assembled Editing Complexes
93
3.6
Concluding Remarks
96
Acknowledgments
96
References
96
CHAPTER
4
MACHINERY OF
RNA
EDITING IN
ΡΙΛΝΤ
ORGANELLES
99
4.1
Introduction
99
4.2
Mechanism of Target Recognition
100
4.3
PPR
Protein is a Trans-Factor in Plastids
101
4.4
How Can the Model Be Generalized to Plant
RNA
Editing?
104
4.5
Can Closely Located Editing Sites Share
a íraraí-Factor?
105
CONTENTS
VII
4.6
Is a Trans-Factor Specific to a Single Cis-Element?
106
4.7
Mechanism Determining the Efficiency of
RNA
Editing
107
4.8
Co-Evolution of Tram-Factors and Editing Sites
109
4.9
What is an Editing Enzyme?
110
4.10
A Model of Editing Machinery in Plastids
112
4.11
Future Directions
114
Acknowledgments
114
References
114
part
и
FUNCTIONAL COORDINATION OF
RNA
EDITING
WITH OTHER CELLULAR MECHANISMS
CHAPTER
5
TRANSFER
RNA
EDITING ENZYMES; AT THE CROSSROADS
_
OF AFFINITY AND SPECIFICITY
_123
5.1
Introduction: Structural Versus Functional tRNA Editing
123
5.2
Transfer
RNA
Editing for Structure
124
5.2.1
C-to-U Editing of the tRNA Backbone
124
5.2.2
A-to-I Editing and Modification at Position
37
and
57
of tRNAs
126
5.3
Transfer
RNA
Editing for Function
127
5.3.1
The Lysidine Story
127
5.3.2
Nucleotide Additions at the Ends of tRNAs
130
5.3.3
C-to-U Editing in Marsupials and Trypanosomatids
133
5.3.4
A-to-I Editing of tRNAs in Yeast and Bacteria
137
5.3.5
Double Editing in Trypanosomatids
139
5.4
The Transfer
RNA
Editing Enzymes of Trypanosomatids:
A Special Case of Catalytic Flexibility
140
5.5
Complex Formation by Transfer
RNA
Editing Enzymes:
A Model for the Regulation of Editing Activity
141
5.6
Concluding Remarks: Evolution of Transfer
RNA
Editing
Deaminases: Affinity Versus Specificity
142
References
143
CHAPTER
6
A-TO-I EDITING AS A CO-TRANSCRIPTIONAL
RNA
_
PROCESSING EVENT
_146
6.1
Introduction
146
6.1.1
Overview of Co-transcriptional Pre-mRNA Processing
147
6.1.2
Localization of the ADAR Proteins
148
6.1.3
A-to-I Editing as a Pre-mRNA Processing Event
149
6.2
Main Questions in the Field and Approaches
149
6.2.1
Why Are Edited Sites Often Situated Close to
Exon/bitron
Border?
149
6.2.2
The Potential of A-to-I Editing in Changing the
Transcriptome
151
6.2.3
RNA
Editing, the Influence on Pre-mRNA Splicing and Vice Versa
152
6.3
Can Editing Influence the Fate of a Messenger
RNA
in Other Ways?
156
6.3.1
Editing and Its Potential Effect on
RNA
Export
156
6.3.2
Editing as a Modulator of
RNA
Stability
156
6.3.3
Editing and Its Influence on Polyadenylarion
157
6.4
Prospectives
for Future Research
158
References
159
VIII CONTENTS
CHAPTER
7
STUDYING AND WORKING WITH RIBONUCLEOPROTEINS
_
THAT CATALYZE H/ACA GUIDED
RNA
MODIFICATION
_162
7.1
Introduction
162
7.2
Discovery of Complex (RNA-guided) Pseudouridine Synthases
164
7.3
Approaches and Challenges
164
7.4
RNP
Reconstitution
166
7.5
Lessons from Archaeal H/ACA RNPs
167
7.6
Biogenesis ofEukaryotic H/ACA RNPs
168
7.7
Debate on Dyskeratosis
Congenita
168
7.8
Importance and Future of H/ACA RNPs
169
Acknowledgments
170
References
171
CHAPTER
8
FUNCTIONAL ROLES OF SPLICEOSOMAL snRNA
_
MODIFICATIONS IN PRE-mRNA SPLICING
_175
8.1
Introduction
175
8.2
Modified Nucleotides in Spliceosomal snRNAs
176
8.3
Functional Analysis of Spliceosomal snRNA Modifications
179
8.4
Modified Nucleotides of U2 snRNA are Important
for
Ргє
-mRNA
Splicing
180
8.5
U2 Modifications Contribute to snRNP Biogenesis
and Spliceosome Assembly
182
8.6
Genetic Analysis of
Ш
Modification in Yeast
183
8.7
Cytotoxicity Associated with 5FU Treatment is a Result of Inhibition
on Pseudouridy
lation
and Splicing
184
8.8
Biophysical Analysis of U2 snRNA Modification
185
8.9
Concluding Remarks
186
References
186
CHAPTER
9
A ROLE FOR A-TO-I EDITING IN GENE SILENCING
_190
9.1
Expression of Double-Stranded
RNA
in Cells
190
9.2
The Activity of ADAR in the Nucleus
191
9.3
Alternative Fates of Edited RNAs in the Nucleus
192
9.4
A Possible Connection Between
RNA
Editing and Gene Silencing
193
9.4.1
Heterochromatin
193
9.4.2
RNAi-Directed Heterochromatin Formation
194
9.4.3
Connections Between RNAi and dsRNA Editing
196
9.4.4
Vigilin
196
9A5 Recognition of
RNA
by Vigilins
197
9.4.6
The Vigilin Complex
198
9.5
A Model for the Nuclear Function of Vigilin
199
References
200
CHAPTER
10
BIOWGICALIMPUCATIONS AND BROADER-RANGE FUNCTIONS
FORAPOBEC-l ANDAPOBEC-l COMPIlSMENTAimN
_
FACTOR (ACF)
_
10.1
Overview
203
CONTENTS
IX
10.2
Background to Our Current Understanding of C-to-U Editing of ApoB mRNA:
Canonical Functions for Apobec-l andACF
204
10.2.1
Role of
Cis-
Acting Elements
204
10.2.2
Identification and Characterization of Trans-Acting Factors
206
10.3
Current Understanding of Apobec-l and ACF: Structure-Function
and Genetic Regulation
209
10.3.1
Apobec-l: Structure-Function Relationships
209
10.3.2
Functions of Apobec-l Beyond apoB mRNA Editing
210
10.3.3
Apobec-l: Genetic Regulation and Gain-and Loss-of-Function
212
10.3.4
ACF: Structure-Function Relationships
214
10.3.5
Intersections of Apobec-l and ACF Regulation in the Modulation
of C-to-U
RNA
Editing
216
10.4
Implications and Broad-Range Function for Apobec-l and ACF:
Future Directions and Overarching Questions
218
10.4.1
Apobec-l
218
10.4.2
ACF
220
10.5
Conclusions
224
Acknowledgments
224
References
224
CHAPTER
1
\ ANTIVIRAL FUNCTION OF APOBEC3 CYTIDINE DEAMINASES
231
11.1
Explanation of
Vif Phenotype
Uncovers a Unique Innate Resistance to
HIV-1 Infection
231
11.2
Antiviral Functionality of the APOBEC3 Family of Proteins
232
11.2.1
Mechanism of Action
232
11.2.2
APOBEC3 Proteins and the Prevention of Zoonosis
235
11.2.3
In Vivo Correlations Between APOBEC3 Expression and Disease Course
236
11.3
The Battle for Control: Viral Suppression of the APOBEC3 Proteins
237
11.3.1
The Hijacking of the Proteasomal Degradation Pathways
237
11.3.2
Virion Exclusion of the APOBECs via a Viral-Dependent Mechanism
238
11.4
Cellular Function and Regulation of the APOBEC3 Family
238
11.4.1
Guardians of the Genome:
АРОВЕСЗ
-Međiated
Suppression
of Cellular Retroelements
238
11.4.2
Subcellular Localization (Sequestration)
239
11.4.3
Control of the Expression of the APOBEC3 Family is Exerted
Transcriptionally
240
11.5
Research Questions and the Hope of Therapeutic Manipulation of the
APOBEC3 Family
243
11.5.1
The "Alternative Function"
244
11.5.2
Protein Partitiomng/Subcellular Localization
245
11.5.3
Protein Cofactors and Posttranslational Modifications
245
11.5.4
Therapeutic Potential
246
References
247
PARTHt PMBicmm structures
CHAPTER
12
A-TO-I EDITING OF Aim REPFATS
_257
12.1
Background
257
12.1.1
Indirect Evidence for Abundant A-to-I Editing
257
X
CONTENTS
12.1.2
Early Screens for A-to-I Editing Targets
258
12.1.3
The
Alu
Repeats
259
12.2
Computational Detection of A-to-I Editing
260
12.2.1
Sifting through
db EST
260
12.2.2
Clusters of Mismatches in RNAs
262
12.2.3
Numbers of Editing Sites Detected
265
12.2.4
Characterization of the Edited Transcripts
265
12.2.5
Looking for Conserved Polymorphism Sites
267
12.2.6
Additional Potential Targets for Abundant A-to-I Editing
267
12.3
Editing in Other Organisms
268
12.3.1
Uniqueness of the
Alu
Repeat
269
12.3.2
Predicting Editing Sites from Genomic Data
270
12.4
Biological Role of
Afe
Editing
272
12.4.1
Possible Regulatory Roles
272
12.4.2
Alu
Editing and miRNA
272
12.4.3
Alternative Splicing and
Alu
Editing
273
12.5
Concluding Remarks
275
References
276
CHAPTER
13
RNA
EDITING IN DINOFLAGELLATES AND ITS IMPLICATIONS
FOR THE EVOLUTIONARY HISTORY OF THE
_
EDITING MACHINERY
_280
13.1
Introduction
280
13.2
Inferred
RNA
Editing in Dinoflagellates
283
13.2.1
cob and
««7
mRNA
283
13.2.2
Chloroplast Transcripts
288
13.3
Biochemical Characteristics of Editing
289
13.3.1
Unusually Diverse Types of Editing
289
13.3.2
Varying Editing Density and Discrete Distribution of Editing Events
in Coding Sequences
293
13.3.3
Markedly Nonrandom Distribution in the Type of Codon Edited
and in the Position of the Editing Site Within
Codons
294
13.4
Consequences of Editing
297
13.5
Phylogenetic Trend
301
13.6
Implications for the Origin and Evolution of the
RNA
Editing Machinery
304
Acknowledgment
306
References
306
part
iv
STRUCTURAL APPROACHES
CHAPTER
14
THE BOX C/D RNPs: EVOLUTIONARILY ANCIENT
_
NUCLEOTIDE MODIFICATION COMPLEXES
_313
14.1
Introduction
313
14.2
Diversity of Box
C/D RNA
Populations
314
14.2.1
Box
C/D RNA
Nomenclature
314
14.2.2
Box
C/D RNA
Structure
315
CONTENTS
XI
14.2.3
Diversity of Box
C/D RNA
Populations
316
14.2.4
Box
C/D RNA
Identification
316
14.3
Box
C/D RNA
Functions and Target RNAs
319
14.3.1
Folding and Cleavage of Pre-rRXA
319
14.3.2
^-O-Methylation of Diverse
RNA
Targets
319
14.3.3
Additional Roles and Targets for Box CD RNAs
320
14.4
Box C/D RNP Structure and Nucleotide Methylation Function
321
14.4.1
Eukaryotic Box C/D Core Proteins and snoRNP Structure
321
14.4.2
Archaeal Box C/D Core Proteins and In Vitro sRNP
Assembly
322
14.4.3
Emerging Core Protein and RNP Crystal Structures
322
14.4.4
Investigating Methylation Function Using In Vitro Assembled
Archaeal Box C/D sRNP
323
14.5
Box C/D RNP Biogenesis
323
14.5.1
Genomic Organization of Eukaryotic Box C/D snoRNA Genes
323
14.5.2
Independently Transcribed and Intronic Eukaryotic Box C/D
snoRNA Genes
324
14.5.3
Archaeal Box C/D sRNA Genes
324
14.5.4
Transcription and Processing of Independently Transcribed
Box C/D snoRNAs
325
14.5.5
Transcription and Processing of Intronic Box C/D
snoRNAs
326
14.5.6
Box C/D snoRNP Transport
327
14.6
Future Directions and Experimental Challenges
327
14.6.1
Box C/D
RNA
Diversity, Targets, and Functions
327
14.6.2
Box C/D RNP Structure and Methylation Function
328
14.6.3
Box C/D RNP Biogenesis
330
Acknowledgments
331
References
331
CHAPTER
15
STRUCTURAL FEATURES OF THE ADAS. FAMILY
_
OF ENZYMES AND THEIR SUBSTRATES
_ 340
15.1
ADAR Enzymes
340
15.2
Overview and Functions of ADARs
341
15.2.1
Double-Stranded
RNA
Binding Domains (dsRBDs)
344
15.2.2
Xenopus laevis XIrbpa
345
15.2.3
ADAR2 dsRBDl and dsRBD2
346
15.2.4
Deaminase Domain
346
15.2.5
Za
and
Zß
Domains
347
15.2.6
Za
Structure
349
15.2.7 Zß
Structure
351
15.2.8
Structural Comparison of
Za
and
Zß 354
15.3
Conclusions
354
15.4
Substrates
355
15.4.1
Overview and General Features
355
15.5
Double-Stranded
RNA
Targets and Structural Features
355
15.5.1
Site-Selective A-to-I Editing
355
15.5.2
Structural Features of Site-Selective A-to-I Editing
358
15.5.3
Promiscuous Editing
359
XII CONTENTS
15.6
Single-stranded
RNA
Targets 361
15.7
Z-DNA and Z-RNA Targets
361
15.8
Future Directions
362
References
362
CHAPTER
16
CHEMISTRY, PHYLOGENY, AND THREE-DIMENSIONAL
_
STRUCTURE OF THE APOBEC PROTEIN FAMILY
_369
16.1
Introduction to Nucleic Acid Deamination with Implications
for Biological Activity
369
16.2
The Chemistry of the Zinc-Dependent Deaminase
Amino
Acid
Signature Motif
370
16.3
The ZDD Signature Motif Implies a Specific Three-Dimensional
Arrangement of
Amino
Acids
371
16.4
Rationale for a Combined Structural and Phylogenetic Approach to
Understand APOBEC Evolution
373
16.4.1
The Starting Point for Structural and Phylogenetic Analyses of
APOBEC Family Members
375
16.4.2
The
CDA
Superfamily: Overview of Conserved Fold Topology in the
Core and Common Variations
379
16.4.3
Comparison of the Common
CDA
Superfamily Core Reveals
Broad Peripheral Diversification
381
16.5
Modes of Oligomerization
382
16.5.1
Free Nucleotide Cytidine Deaminases
(CDA):
Strand
ß5 Antiparallel
to Strand
Џ
382
16.5.2
Cytosine Deaminase, Guanine Deaminase, and TadA:
Strand
ß5
Parallel to
Џ
382
16.5.3
Deoxcytidylate Deaminases (T4,
N.
e) and APOBEC2:
Strand
ß5
Parallel to
ß4 383
16.5.4
Multidomain Enzymes RibG and ADAR2 of the
CDA
Superfamily:
Strand
ß5
Parallel to
ß4 387
16.6
Modes of Substrate Interaction
388
16.6.1
Tetrameric fnCDAs Favor Flexible Flaps:
RNA
Editing and the
Case of Cddl from Yeast
390
16.6.2
A Topological Transformation Obstructs Active Site Accessibility
in Dimerie Deaminases that Bind Bases
391
16.6.3
Substrate Selection by Polynucleotide Editing Enzymes
Remains Elusive
391
16.7
The APOBEC Family: Insights into a Structurally Underrepresented Family
392
16.7.1
Activation-Induced Deaminase (AID)
—
an Ancient Enzyme
with Essential Roles in Adaptive Immunity
395
16.7.2
APOBEC2
—
A Divergent Ancestral Protein of Unknown Function
396
16.7.3
APOBECl—The Historical Archetype of C-to-U Editing Enzymes
397
16.7.4
APOBEC4
—
Pushing the Envelope of APOBEC Boundaries
399
16.8
APOBEC3—
Radiative Expansion of Proteins Involved in Viral Defense
400
16.8.1
Mechanisms of Primate-Specific Expansion of the APOBEC3 Proteins
402
16.8.2
Alternative Methods to Obtain Structure: The Molecular Envelope
of
АРОВЕСЗО
by Small-Angle
Х
-Ray Scattering
405
16.8.3
Characterization of Structural Changes in
АРОВЕСЗО
Morphology
in the Presence of
RNA
406
CONTENTS XIII
16.8.4 Positive
Selection Exerted on the APOBEC3 Family
408
16.9
Conclusions and Future Prospects
410
References
411
INDEX
421 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| building | Verbundindex |
| bvnumber | BV023303865 |
| callnumber-first | Q - Science |
| callnumber-label | QH450 |
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| ctrlnum | (OCoLC)173469796 (DE-599)BVBBV023303865 |
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| dewey-hundreds | 500 - Natural sciences and mathematics |
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| discipline_str_mv | Biologie |
| format | Book |
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| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV023303865 |
| illustrated | Illustrated |
| index_date | 2024-07-02T20:47:40Z |
| indexdate | 2024-07-09T21:15:24Z |
| institution | BVB |
| isbn | 9780470109915 |
| language | English |
| lccn | 2007039289 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016488270 |
| oclc_num | 173469796 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-703 DE-11 |
| owner_facet | DE-355 DE-BY-UBR DE-703 DE-11 |
| physical | XXIII, 426 S. Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | Wiley-Interscience |
| record_format | marc |
| spelling | RNA and DNA editing molecular mechanisms and their integration into biological systems ed. by Harold C. Smith Hoboken, N.J. Wiley-Interscience 2008 XXIII, 426 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Base Sequence DNA Genetic transcription Genomics Nucleotide sequence RNA Editing RNA editing Transcription, Genetic Transkription Genetik (DE-588)4185906-6 gnd rswk-swf RNS-Edierung (DE-588)4350250-7 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content RNS-Edierung (DE-588)4350250-7 s DE-604 Transkription Genetik (DE-588)4185906-6 s b DE-604 Smith, Harold C. Sonstige oth Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016488270&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | RNA and DNA editing molecular mechanisms and their integration into biological systems Base Sequence DNA Genetic transcription Genomics Nucleotide sequence RNA Editing RNA editing Transcription, Genetic Transkription Genetik (DE-588)4185906-6 gnd RNS-Edierung (DE-588)4350250-7 gnd |
| subject_GND | (DE-588)4185906-6 (DE-588)4350250-7 (DE-588)4143413-4 |
| title | RNA and DNA editing molecular mechanisms and their integration into biological systems |
| title_auth | RNA and DNA editing molecular mechanisms and their integration into biological systems |
| title_exact_search | RNA and DNA editing molecular mechanisms and their integration into biological systems |
| title_exact_search_txtP | RNA and DNA editing molecular mechanisms and their integration into biological systems |
| title_full | RNA and DNA editing molecular mechanisms and their integration into biological systems ed. by Harold C. Smith |
| title_fullStr | RNA and DNA editing molecular mechanisms and their integration into biological systems ed. by Harold C. Smith |
| title_full_unstemmed | RNA and DNA editing molecular mechanisms and their integration into biological systems ed. by Harold C. Smith |
| title_short | RNA and DNA editing |
| title_sort | rna and dna editing molecular mechanisms and their integration into biological systems |
| title_sub | molecular mechanisms and their integration into biological systems |
| topic | Base Sequence DNA Genetic transcription Genomics Nucleotide sequence RNA Editing RNA editing Transcription, Genetic Transkription Genetik (DE-588)4185906-6 gnd RNS-Edierung (DE-588)4350250-7 gnd |
| topic_facet | Base Sequence DNA Genetic transcription Genomics Nucleotide sequence RNA Editing RNA editing Transcription, Genetic Transkription Genetik RNS-Edierung Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016488270&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT smithharoldc rnaanddnaeditingmolecularmechanismsandtheirintegrationintobiologicalsystems |