Regulatory RNA:
Gespeichert in:
| Späterer Titel: | RNA motifs and regulatory elements |
|---|---|
| Hauptverfasser: | , |
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
1998
|
| Schriftenreihe: | Biotechnology intelligence unit
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | 262 S. graph. Darst. |
| ISBN: | 3540643435 |
Internformat
MARC
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Datensatz im Suchindex
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|---|---|
| adam_text | I CONTENTS =r
1. An Introduction to Regulatory RNA Motifs 1
A Short Guide to the Book 1
A Look Back: RNA, the Magic Molecule 2
RNA Motifs in RNA Information Flow and RNA Catalysis.... 4
Fig. l.i. Regulatory motifs in mRNA metabolism 6
Fig. 1.2. Two examples for RNA motifs (RRE.TAR) 7
Regulation of Gene Expression at the Level of the RNA 10
Time or space dependent information release by RNA 10
Catalysis and processing involving RNA 12
Ribonudeoproteins: Combination of RNA and proteins 13
RNA Motifs as a Tool to Look for Conserved Function 14
Perspective: Context Specificity of RNA Within the Cell 15
2. Instances of Functional RNA (An Overview) 19
Introduction 19
The Different Types of RNA 20
Table 2.1. The different types of RNA (overview) 20
General Nuclear RNA Binding Motifs
and Nucleoproteins 22
RNA and RNA Motifs Involved in Splicing 24
RNA protein interactions; Fig. 2.1, rRNA 26
Fig. 2.2, snRNAs 27
Further variants: Selfsplicing introns 27
Trans splicing 28
Editing 28
Motifs and RNAs Involved
in Ribosomal RNA Processing 28
Post Transcriptional Regulatory Signals in m RNA 29
5 UTR 29
Regulatory signals in the open reading frame 30
Translation regulated by non mRNA 30
Modified residues in eukaryotic messenger mRNA 31
Correction of missing stop codons by loSa RNA or tm RNA 31
The 3 UTR of Messenger RNA 31
3 UTR of mRNA (Fig. 2.3, LOX mRNA) 33
Fig. 2.4,3 processing motifs 34
Direct Regulation of Gene Expression 35
Autoregulatory RNA 35
AntisenseRNA 36
Regulation of prokaryotic operons 36
Cytoplasmic RNA and Motifs 37
Ribozymes and Their Motifs 38
Viral RNA 38
Other RNA Species 40
A Catalogue of Regulatory RNA 40
Table 2.2 a) Well characterized motifs 41
Table 2.2 b) Complex motifs 46
Figures of Specific Motifs 48
Se Cys mRNA; Fig. 2.5 transferrin receptor mRNA 48
Fig. 2.6, developmental RNA motifs 48
5 UTR of mRNA, Fig. 2.7, eukaryotic iron responsive elements 49
Fig. 2.8, prokaryotic translational repression, a mRNA 50
Correcting mRNA translation (Fig. 2.9, loSa RNA/tmRNA) 51
Splicing Fig. 2.10, simple and 52
Fig. 2.10b, detailed pathway 53
Fig. 2.n,U6/U4 and U6/U2 54
Fig. 2.11b, U5 loop 55
Fig. 2.12, Ui/U6/U2/pre mRNA 55
Fig. 2.13, alternative splice site selection 56
trans splicing Fig. 2.14, leader mRNAs and reaction 57
Small nudeolar RNAs; Fig. 2.15 58
Fig. 2.16, guide snoRNAs 59
Viral RNAs (Fig. 2.17) 60
Antisense RNAs (Fig. 2.18, motifs;) 61
Fig. 2.19, RNA III 62
Catalytic RNAs (Fig. 2.20, hammerhead; Fig. 2.21, hairpin) 63
RNAseP (Fig. 2.22, RNA cage) 64
Substrates in Fig. 2.23 65
Selfsplicing introns (group I Fig. 2.24, group II Fig. 2.25) 66,67
Selfsplicing intron reactions (Fig. 2.26) 68,69
Cytoplasmic RNAs (Fig. 2.27,7S RNA from SRP) 70
Many RNA Motifs Together: RNA Viridae 70
Table 2.3 Classification of different RNA viridae 71
Table 2.4 Important protein motifs recognizing RNA 72
Protein Motifs Pointing to Interacting RNA Structures 72
Modified Nudeotides 72
Table 2.5 RNA modifications 73
Perspective: From Known Instances to New Ones 73
3. Experimental Identification of New Functional RNA 85
Introduction 85
Typical Settings 87
Revealing RNAs as Key Players in Cellular Regulation 89
Double stranded RNA in growth arrest 90
Revealing regulatory structures in developmental RNAs 90
Identification of further translational regulatory mRNA motifs 91
Affinity screens to reveal RNA interaction with proteins 94
Crosslinking to reveal RNA interaction with proteins 94
Direct Confirmation of RNA Functionality 95
Detailed probing of an RNA motif 95
Revealing the exact RNA structure 96
Finding RNA Motifs for a Desired Task 97
RNA SELEX experiments 97
Further approaches to design and engineer RNA 99
Perspective: Future Directions 99
Fig. 3.1 SELEX method and subsequent genomic search 100
4. Computer Based and Theoretical Identification
of Regulatory RNA 105
Introduction 105
Steps Involved in an RNA Motif Search 106
Describe the motif 106
Identify common features 107
Derive a consensus pattern 107
From the analytical description to the search program 108
Fig. 4.1 Consensus patterns 109
Program tests no
Analyzing program output 111
Comparing promising candidate structures and known examples in
Experimental and further tests for remaining best candidate 112
A Typical Example 113
Specific Motif Search Programs 114
General Purpose Search Programs 117
Evaluation of the Search Result 121
The best candidate RNA structures 123
Table 4.1. Reducing the number of RNA candidate structures 123
Generalized Searches for RNA Motifs 124
Table 4.2. Some points to check during an RNA motif search 125
Perspective: An Incentive 128
5. Functional RNA Interactions 133
Introduction 133
Control of Information Release 133
Catalysis 136
Metabolism 137
Evolution 139
Protein—RNA Interactions 140
Table 5.1. Examples of RNA specific protein interactions 141
Modified Nucleotides in RNA 142
Identification of modified nucleotides 143
Modified nucleotides as tools to modulate RNA metabolism 143
(Table 5.2. Some examples) 144
Dynamics 144
Further Development 147
Nanopatterns using oligonudeotides 148
Artificial evolution of peptides coupled to UNA SELEX 149
Medical Implications: Curing RNA by Trans Splicing 149
Medical Implications: Antisense Approaches 150
Ribozyme mediated RNA repair (Fig. 5.1) 151
Medical Implications: Ribozymes 154
Hammerheads 154
Medical Manipulation of Ribonucleoprotein Particles 155
Targeting of RNA, Fig. 5.2 155
Suggestions for Further Therapies 156
Perspectives 156
New targets 156
Translational inhibition 157
Understanding RNA tools 157
6. Areas of Research on Regulatory RNA
and Functional RNA Motifs 165
Introduction 165
The Splicing of Messenger RNA 165
Process and RNA recognition 166
ATAC introns (Fig. 6.1) 168
7 «ws Splicing 169
RNA Editing 171
Mammalian RNA editing 172
Fig. 6.2 RNA editing examples 173
Editing in trypanosomes 174
in slime mold physarum 175
in plant mitochondria and chloroplasts 175
in hepatitis delta virus 176
Ribosomal RNA Processing and Ribosome Biogenesis 177
A focus of interest 177
Ribosomal RNA processing steps 178
Pathway (Fig. 6.3) 179
snoRNAs 181
Nuclear RNA Transport 183
Messenger RNA and Regulatory Motifs:
The 5 Untranslated Region in mRNA 184
Open Reading Frames in mRNA 186
Is a cDNA sequence complete? 186
Regulation of ORF translation by transfer RNA redundancy 187
The 3 Untranslated Region in mRNA 187
3 UTR in parasites 187
Se CysmRNAs 188
Motif searches and a SELEX approach 188
Detailed analysis of a complex RNA stability motif in the 3 UTR 189
Polyadenylation signals 190
Developmental differentiation signals in the 3 UTR 190
Three hybrid screening system (Fig. 6.4) 191
Developmental localization signals in the 3 UTR 192
Catalytic RNAs 193
Selfsplicing introns 194
Viral RNAs 195
Perspective: New Interesting RNA Structures 196
Cytoplasmic RNAs 196
XIST, (X chromosome inactivation) RNA 196
H19 RNA and imprinting 198
C. elegans lin 4 RNA 199
Telomerases: maintaining the ends of the chromosomes 200
Fig. 6.5. Telomerase RNA and telomers 201
Small RNAs in E. coli 202
OxyS (Fig. 6.6) 203
7. Future Research 221
Introduction 221
Splicing 221
Editing, Trans Splicing and Beyond 222
Ribosomal RNA and Cofactors 223
Signals in the mRNA 223
Antisense RNA 224
Biotechnological Applications 225
Conclusion 225
Alphabetical References 227
Index 257
|
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| author | Dandekar, Thomas 1960- Sharma, Kishor |
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| bvnumber | BV012044851 |
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| id | DE-604.BV012044851 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T18:20:41Z |
| institution | BVB |
| isbn | 3540643435 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-008151866 |
| oclc_num | 245742781 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-12 DE-634 |
| owner_facet | DE-355 DE-BY-UBR DE-12 DE-634 |
| physical | 262 S. graph. Darst. |
| publishDate | 1998 |
| publishDateSearch | 1998 |
| publishDateSort | 1998 |
| publisher | Springer |
| record_format | marc |
| series2 | Biotechnology intelligence unit |
| spelling | Dandekar, Thomas 1960- Verfasser (DE-588)120961059 aut Regulatory RNA Thomas Dandekar ; Kishor Sharma Berlin [u.a.] Springer 1998 262 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biotechnology intelligence unit RNS - Genregulation RNS (DE-588)4076759-0 gnd rswk-swf Genregulation (DE-588)4122166-7 gnd rswk-swf RNS (DE-588)4076759-0 s Genregulation (DE-588)4122166-7 s DE-604 Sharma, Kishor Verfasser aut 2. Aufl. u.d.T. RNA motifs and regulatory elements HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=008151866&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Dandekar, Thomas 1960- Sharma, Kishor Regulatory RNA RNS - Genregulation RNS (DE-588)4076759-0 gnd Genregulation (DE-588)4122166-7 gnd |
| subject_GND | (DE-588)4076759-0 (DE-588)4122166-7 |
| title | Regulatory RNA |
| title_auth | Regulatory RNA |
| title_exact_search | Regulatory RNA |
| title_full | Regulatory RNA Thomas Dandekar ; Kishor Sharma |
| title_fullStr | Regulatory RNA Thomas Dandekar ; Kishor Sharma |
| title_full_unstemmed | Regulatory RNA Thomas Dandekar ; Kishor Sharma |
| title_new | RNA motifs and regulatory elements |
| title_short | Regulatory RNA |
| title_sort | regulatory rna |
| topic | RNS - Genregulation RNS (DE-588)4076759-0 gnd Genregulation (DE-588)4122166-7 gnd |
| topic_facet | RNS - Genregulation RNS Genregulation |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=008151866&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT dandekarthomas regulatoryrna AT sharmakishor regulatoryrna |