MicroRNA methods:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2007
|
| Series: | Methods in enzymology
427 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XL, 261 S., [4] Bl. Ill., graph. Darst. |
| ISBN: | 9780123739179 |
Staff View
MARC
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| 245 | 1 | 0 | |a MicroRNA methods |c ed. by John J. Rossi ... |
| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2007 | |
| 300 | |a XL, 261 S., [4] 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 427 | |
| 650 | 4 | |a MicroRNAs | |
| 650 | 4 | |a RNA, Messenger |x physiology | |
| 650 | 4 | |a Sequence Analysis, RNA | |
| 650 | 4 | |a Small interfering RNA | |
| 650 | 0 | 7 | |a Labortechnik |0 (DE-588)4123602-6 |2 gnd |9 rswk-swf |
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| 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=015957682&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
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Record in the Search Index
| _version_ | 1804136997660393472 |
|---|---|
| adam_text | Contents
Contributors
xi
Volumes in Series
xv
Section I. Identifying
M
¡ero
R N
As and Their Targets
ι
1. Identification of Viral MicroRNAs
3
Christopher S. Sullivan and Adam
Grundhoff
1.
Introduction
3
2.
Computational Prediction of Viral miRNA Candidates
7
3.
Array Confirmation of Viral miRNA Candidates
11
4.
Concluding Remarks
21
References
22
2.
Robust Machine Learning Algorithms Predict
MicroRNA Genes and Targets
25
Pål Saätrom
and Ola
Snove,
Jr.
1.
Introduction
26
2.
Appropriate Use of Machine Learning
27
3.
One Deterministic and One Stochastic Algorithm
33
4.
miRNA Gene Prediction with Support Vector Machines
37
5.
miRNA Target Prediction with Boosted Genetic Programming
43
6.
Summary
46
Acknowledgments
46
References
46
3.
Identification of Virally Encoded MicroRNAs
51
Sébastien
Pfeffer
1.
Introduction
52
2.
Purification of Rnb
(1-249)
ar|d Adenylation of
3
Adapter Oligonucleotide
55
3.
Isolation of the Small
RNA
Fraction
55
4.
Ligation of the Purified Small
RNA
to Adenylated
3
Adapter
56
5.
Ligation of the Small RNA-3 Adapter to the
5
Adapter
56
6.
Reverse Transcription of the Final Ligation Product
57
vi
Contents
7.
First PCR
Amplification
of the cDNA
57
8.
Pme
/
Digestion of the PCR Product
58
9.
Second PCR Amplification
58
10.
Ban
/
Digestion of the Second PCR Product
59
11.
Concatamerization of the Ban/-Digested
DNA 59
12.
End Tailing of Concatamers and Cloning into T/A Vector
59
13.
Sequencing and Annotation of the Library
60
14.
Concluding Remarks
60
References
61
4.
Computational Methods for MicroRNA Target Prediction
65
Yuka Watanabe, Masaru
Tornita,
and Akio Kanai
1.
Introduction
66
2.
Principles of miRNA Target Recognition
69
3.
Resources for Analysis of miRNA Target Genes
73
4.
Software Useful for miRNA Target Prediction
74
5.
Original Strategies for Prediction of miRNA Target Genes
79
6.
Validation of Computational Predictions
81
7.
Concluding Remarks
82
Acknowledgments
83
References
83
Section II. MicroRNA Expression, Maturation,
and Functional Analysis
87
5.
In Vitro and In Vivo Assays for the Activity of
Drosha Complex
89
Yoontae Lee and V. Narry Kim
1.
Introduction
89
2,
Assay Methods
94
Acknowledgments
105
References
105
6.
Microarray Analysis of miRNA Gene Expression
107
J. Michael Thomson, Joel S. Parker, and Scott M. Hammond
1.
Introduction
107
2.
Overview of miRNA Biogenesis and Effector Pathways
109
3.
miRNA Expression Analysis Strategies
110
4.
Considerations for miRNA Microarrays
111
5.
Data Analysis and Interpretation
112
Contents
vii
6.
Validation
Strategies
113
7.
rníRNA Microarray
Protocol
113
8.
Data Analysis
118
Acknowledgments
119
References
119
7.
Cloning and Detecting Signature MicroRNAs from
Mammalian Cells
123
Guihua Sun, Haitang Li, and John J. Rossi
1.
Introduction
124
2.
miRNA Cloning
126
3.
miRNA Identification
133
4.
Northern Hybridization to Verify In Vivo Expression of miRNA
134
Acknowledgments
136
References
136
8.
Approaches for Studying MicroRNA and Small Interfering
RNA
Methylation In Vitro and In Vivo
139
Zhiyong Yang, Giedrius Vilkaitis, Bin Yu,
Saulius
Klimašauskas,
and Xuemei Chen
1.
Introduction
140
2.
Expression and Purification of
Recombinant
HENi Proteins
141
3.
Small
RNA
Methyttransferase Assays with
Recombinant
HENi Proteins
144
4.
Reverse-Phase HPLC Analysis to Determine the
Position of the Methyl Group in Products of
HENi-Catalyzed Reactions
148
5.
Immunoprecipitation and HENi Activity Assay
149
6.
Analysis of the In Vivo Methylation Status of miRNAs and siRNAs
151
7.
Concluding Remarks
152
Acknowledgments
152
References
153
9.
Analysis of Small
RNA
Profiles During Development
155
Toshiaki Watanabe, Yasushi Totoki, Hiroyuki Sasaki,
Naojiro
Minami,
and Hiroshi Imai
1.
Introduction
156
2.
Preparation of Low-Molecular-Weight
RNA
and
Urea-Polyacrylamide Gel Electrophoresis (Urea-PAGE)
158
3.
Cloning of Small RNAs
161
viii Contents
4.
Classification
of Small RNAs
163
5.
Northern Blot Analysis
165
References
167
10.
Dissecting MicroRNA-mediated Gene Regulation and
Function in
Т
-Cell
Development
171
Tin Ky Mao and Chang-Zheng Chen
1.
Introduction
172
2.
Characterizing miRNA Expression During
Т
-Cell
Development
172
3.
Retroviral Constructs for miRNA Expression
178
4.
Investigating miRNA Function in
Т
-Cell
Development
180
5.
Identification and Validation of Functionally
Relevant miRNA Target Genes
183
6.
Materials and Reagents
187
Acknowledgments
188
References
188
Section III. MicroRNAs and Disease
191
11.
Investigation of MicroRNAs Alterations in
Leukémiás
and Lymphomas
193
George Adrian
Calin
and Carlo Maria
Croce
1.
MicroRNA Alterations are Involved in the Initiation
and Progression of Every Type of Human Cancer
194
2.
Genome-Wide MicroRNA Profiling by Microarray
195
3.
Identification
and Validation of Targets for
Differentially Expressed miRNAs
205
Acknowledgments
210
References
210
12.
Discovery of Pathogen-Regulated Small RNAs in Plants
215
Surekha Katiyar-Agarwal and Hailing Jin
ι.
Introduction
216
2.
Sequencing-Based Approaches for the Discovery
of Pathogen-Regulated Small RNAs
217
3.
Hybridization-Based Approaches of Identifying and
Validating Pathogen-lnducible Small RNAs
219
4.
Concluding Remarks
225
References
226
Contents ix
13.
Protocols for Expression and Functional Analysis
of Viral MicroRNAs
229
Eva
Gottwein
and Bryan R. Cullen
1.
Introduction
230
2.
miRNA Expression Cassettes
232
3.
Vector Systems for Stable Delivery
233
4.
Protocol: Generation of miRNA-Expressing
Cell Lines Using pNL-SIN-CMV-BLR-Based miRNA Expression Vectors
235
5.
Indicator Assays Establish miRNA Activity
237
6.
Protocol: Preparation of Virus Mixes and Indicator Assay
237
7.
Concluding Remarks
240
Acknowledgments
240
References
240
Author Index 24s
Subject Index
257
|
| adam_txt |
Contents
Contributors
xi
Volumes in Series
xv
Section I. Identifying
M
¡ero
R N
As and Their Targets
ι
1. Identification of Viral MicroRNAs
3
Christopher S. Sullivan and Adam
Grundhoff
1.
Introduction
3
2.
Computational Prediction of Viral miRNA Candidates
7
3.
Array Confirmation of Viral miRNA Candidates
11
4.
Concluding Remarks
21
References
22
2.
Robust Machine Learning Algorithms Predict
MicroRNA Genes and Targets
25
Pål Saätrom
and Ola
Snove,
Jr.
1.
Introduction
26
2.
Appropriate Use of Machine Learning
27
3.
One Deterministic and One Stochastic Algorithm
33
4.
miRNA Gene Prediction with Support Vector Machines
37
5.
miRNA Target Prediction with Boosted Genetic Programming
43
6.
Summary
46
Acknowledgments
46
References
46
3.
Identification of Virally Encoded MicroRNAs
51
Sébastien
Pfeffer
1.
Introduction
52
2.
Purification of Rnb
(1-249)
ar|d Adenylation of
3'
Adapter Oligonucleotide
55
3.
Isolation of the Small
RNA
Fraction
55
4.
Ligation of the Purified Small
RNA
to Adenylated
3'
Adapter
56
5.
Ligation of the Small RNA-3' Adapter to the
5'
Adapter
56
6.
Reverse Transcription of the Final Ligation Product
57
vi
Contents
7.
First PCR
Amplification
of the cDNA
57
8.
Pme
/
Digestion of the PCR Product
58
9.
Second PCR Amplification
58
10.
Ban
/
Digestion of the Second PCR Product
59
11.
Concatamerization of the Ban/-Digested
DNA 59
12.
End Tailing of Concatamers and Cloning into T/A Vector
59
13.
Sequencing and Annotation of the Library
60
14.
Concluding Remarks
60
References
61
4.
Computational Methods for MicroRNA Target Prediction
65
Yuka Watanabe, Masaru
Tornita,
and Akio Kanai
1.
Introduction
66
2.
Principles of miRNA Target Recognition
69
3.
Resources for Analysis of miRNA Target Genes
73
4.
Software Useful for miRNA Target Prediction
74
5.
Original Strategies for Prediction of miRNA Target Genes
79
6.
Validation of Computational Predictions
81
7.
Concluding Remarks
82
Acknowledgments
83
References
83
Section II. MicroRNA Expression, Maturation,
and Functional Analysis
87
5.
In Vitro and In Vivo Assays for the Activity of
Drosha Complex
89
Yoontae Lee and V. Narry Kim
1.
Introduction
89
2,
Assay Methods
94
Acknowledgments
105
References
105
6.
Microarray Analysis of miRNA Gene Expression
107
J. Michael Thomson, Joel S. Parker, and Scott M. Hammond
1.
Introduction
107
2.
Overview of miRNA Biogenesis and Effector Pathways
109
3.
miRNA Expression Analysis Strategies
110
4.
Considerations for miRNA Microarrays
111
5.
Data Analysis and Interpretation
112
Contents
vii
6.
Validation
Strategies
113
7.
rníRNA Microarray
Protocol
113
8.
Data Analysis
118
Acknowledgments
119
References
119
7.
Cloning and Detecting Signature MicroRNAs from
Mammalian Cells
123
Guihua Sun, Haitang Li, and John J. Rossi
1.
Introduction
124
2.
miRNA Cloning
126
3.
miRNA Identification
133
4.
Northern Hybridization to Verify In Vivo Expression of miRNA
134
Acknowledgments
136
References
136
8.
Approaches for Studying MicroRNA and Small Interfering
RNA
Methylation In Vitro and In Vivo
139
Zhiyong Yang, Giedrius Vilkaitis, Bin Yu,
Saulius
Klimašauskas,
and Xuemei Chen
1.
Introduction
140
2.
Expression and Purification of
Recombinant
HENi Proteins
141
3.
Small
RNA
Methyttransferase Assays with
Recombinant
HENi Proteins
144
4.
Reverse-Phase HPLC Analysis to Determine the
Position of the Methyl Group in Products of
HENi-Catalyzed Reactions
148
5.
Immunoprecipitation and HENi Activity Assay
149
6.
Analysis of the In Vivo Methylation Status of miRNAs and siRNAs
151
7.
Concluding Remarks
152
Acknowledgments
152
References
153
9.
Analysis of Small
RNA
Profiles During Development
155
Toshiaki Watanabe, Yasushi Totoki, Hiroyuki Sasaki,
Naojiro
Minami,
and Hiroshi Imai
1.
Introduction
156
2.
Preparation of Low-Molecular-Weight
RNA
and
Urea-Polyacrylamide Gel Electrophoresis (Urea-PAGE)
158
3.
Cloning of Small RNAs
161
viii Contents
4.
Classification
of Small RNAs
163
5.
Northern Blot Analysis
165
References
167
10.
Dissecting MicroRNA-mediated Gene Regulation and
Function in
Т
-Cell
Development
171
Tin Ky Mao and Chang-Zheng Chen
1.
Introduction
172
2.
Characterizing miRNA Expression During
Т
-Cell
Development
172
3.
Retroviral Constructs for miRNA Expression
178
4.
Investigating miRNA Function in
Т
-Cell
Development
180
5.
Identification and Validation of Functionally
Relevant miRNA Target Genes
183
6.
Materials and Reagents
187
Acknowledgments
188
References
188
Section III. MicroRNAs and Disease
191
11.
Investigation of MicroRNAs Alterations in
Leukémiás
and Lymphomas
193
George Adrian
Calin
and Carlo Maria
Croce
1.
MicroRNA Alterations are Involved in the Initiation
and Progression of Every Type of Human Cancer
194
2.
Genome-Wide MicroRNA Profiling by Microarray
195
3.
Identification
and Validation of Targets for
Differentially Expressed miRNAs
205
Acknowledgments
210
References
210
12.
Discovery of Pathogen-Regulated Small RNAs in Plants
215
Surekha Katiyar-Agarwal and Hailing Jin
ι.
Introduction
216
2.
Sequencing-Based Approaches for the Discovery
of Pathogen-Regulated Small RNAs
217
3.
Hybridization-Based Approaches of Identifying and
Validating Pathogen-lnducible Small RNAs
219
4.
Concluding Remarks
225
References
226
Contents ix
13.
Protocols for Expression and Functional Analysis
of Viral MicroRNAs
229
Eva
Gottwein
and Bryan R. Cullen
1.
Introduction
230
2.
miRNA Expression Cassettes
232
3.
Vector Systems for Stable Delivery
233
4.
Protocol: Generation of miRNA-Expressing
Cell Lines Using pNL-SIN-CMV-BLR-Based miRNA Expression Vectors
235
5.
Indicator Assays Establish miRNA Activity
237
6.
Protocol: Preparation of Virus Mixes and Indicator Assay
237
7.
Concluding Remarks
240
Acknowledgments
240
References
240
Author Index 24s
Subject Index
257 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
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| illustrated | Illustrated |
| index_date | 2024-07-02T18:31:11Z |
| indexdate | 2024-07-09T21:05:17Z |
| institution | BVB |
| isbn | 9780123739179 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-015957682 |
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| publisher | Elsevier, Acad. Press |
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| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | MicroRNA methods ed. by John J. Rossi ... Amsterdam [u.a.] Elsevier, Acad. Press 2007 XL, 261 S., [4] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 427 MicroRNAs RNA, Messenger physiology Sequence Analysis, RNA Small interfering RNA Labortechnik (DE-588)4123602-6 gnd rswk-swf Small RNA (DE-588)7501213-3 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Small RNA (DE-588)7501213-3 s Labortechnik (DE-588)4123602-6 s DE-604 Rossi, John J. Sonstige oth Methods in enzymology 427 (DE-604)BV000000938 427 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015957682&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | MicroRNA methods Methods in enzymology MicroRNAs RNA, Messenger physiology Sequence Analysis, RNA Small interfering RNA Labortechnik (DE-588)4123602-6 gnd Small RNA (DE-588)7501213-3 gnd |
| subject_GND | (DE-588)4123602-6 (DE-588)7501213-3 (DE-588)4143413-4 |
| title | MicroRNA methods |
| title_auth | MicroRNA methods |
| title_exact_search | MicroRNA methods |
| title_exact_search_txtP | MicroRNA methods |
| title_full | MicroRNA methods ed. by John J. Rossi ... |
| title_fullStr | MicroRNA methods ed. by John J. Rossi ... |
| title_full_unstemmed | MicroRNA methods ed. by John J. Rossi ... |
| title_short | MicroRNA methods |
| title_sort | microrna methods |
| topic | MicroRNAs RNA, Messenger physiology Sequence Analysis, RNA Small interfering RNA Labortechnik (DE-588)4123602-6 gnd Small RNA (DE-588)7501213-3 gnd |
| topic_facet | MicroRNAs RNA, Messenger physiology Sequence Analysis, RNA Small interfering RNA Labortechnik Small RNA Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015957682&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000000938 |
| work_keys_str_mv | AT rossijohnj micrornamethods |