Regulatory RNA

269 Pages·1998·6.954 MB·English

by  Thomas Dandekar, Kishor Sharma (auth.)

Springer
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Thomas Dandekar Kishor Sharma
Regulatory RNA
, Springer
Thomas Dandekar Kishor Sharma
European Molecular European Molecular
Biology Laboratory Biology Laboratory
Heidelberg, Germany Heidelberg, Germany
ISBN 978-3-642.-97995-8
Biotechnology Intelligence Unit
Library of Congress Cataloging-in-Publication data
Dandekar, Thomas, 1960-
Regulatory RNA 1 Thomas Dandekar, Kishor Sharma.
p. cm. - (Biotechnology intelligence unit)
Includes bibliographical references and index.
ISBN 978-3-642-97995-8 ISBN 978-3-642-97993-4 (eBook)
DOI 10.1007/978-3-642-97993-4
1. RNA. 2. Messenger RNA. 3. Genetic regulation. I. Sharma, Kishor, 1969-. II. Title.
III. Series.
[DNLM: 1. RNA-cllemistry. 2. RNA-physiology. 3. Regulatory Sequences, Nucleic
Acid. QU 58.7 D176r 1998)
QU623.D36 1998
572.8'8-dc21
DNLM/DLC 97-44012
for Library of Congress CIP
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DEDICATION
For Gudrun and Jaya
=====PREFACE ======
T
his book provides an introduction and an overview of the field of
regulatory RNA, with a focus on the identification of regulatory
elements and motifs in such RNA molecules. Central to the book is the
use of appropriate techniques to identify regulatory RNA and regula
tory motifs (chapters 3 and 4). The remaining chapters present the motifs
in the context of a more general review on the different areas where
regulatory RNA and regulatory RNA structures are important. The tables
included, in particular Table 2.2 (chapter 2), should provide a quick ref
erence guide to regulatory RNA motifs.
We have made an effort to cover the data in a comprehensive, up
to-date manner. However, it must be kept in mind that as in any other
exciting field in molecular biology, new discoveries are constantly be
ing made in this field, and some topics will have been inadvertently
overlooked. We therefore apologize to our co-workers in the field whose
work could not be incorporated due to limitations of space and time.
Our heartfelt thanks to the numerous colleagues at the EMBL who
have critically read the manuscript and made valuable suggestions. In
particular, we thank Antje Ostareck-Lederer,Dirk Ostareck,Puri Fortes,
Gert- Jan Arts, Jaap Venema, Juan Valcarcel, Giovanni Paollella, Raymond
Post, Martijn Huynen, Mattias Luukonnen, Kostas Pantopoulus, Isabel
Palacios, Petra Riedlinger, Oscar Puig, Josepha Salgado, Mark Nichols,
Rafael Ramirez, Caroline Pope, Livia Merendino, Frank Buchholz, Toby
Gibson,Angus King, Berend Snel, and special thanks to Leonie Ringrose.
We are also grateful to Gudrun Koch and to David Tollervey.
We hope that the book serves as an incentive for the reader, whether
a specialist or a newcomer to the field, to intensify his/her own research
in this exciting field.
CONTENTS
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. 1.1. 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 ............................................. 2.8
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
Antisense RNA ............................................................................................. 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-cl1aracterized 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.lOb, detailed pathway ....................................................................... 53
Fig. 2.n, U6/U4 and U6/U2 ...................................................................... 54
Fig. 2.nb, U5100P ....................................................................................... 55
Fig. 2.12, U1/U6/U2/pre-mRNA ................................................................. 55
Fig. 2.13, alternative splice site selection ................................................. 56
trans-splicing Fig. 2.14, leader-mRNAs and reaction ................................. 57
Small nucleolar 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
RNAse P (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 Nucleotides ................................................................ 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 ............................................................................................... 110
Analyzing program output ......................................................................... 111
Comparing promising candidate structures and known examples ........ 111
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 oligonucleotides ....................................................... 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
Trans-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
~n plant ~itochon~ria and chloroplasts ................................................ 175
m 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-eys mRNAs .......................................................................................... 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
CHAPTER 1
An Introduction to Regulatory
RNA Motifs
A Short Guide to the Book
W
hen collecting examples of regulatory RNA it quickly becomes
apparent that there is a never ending stream of new RNA spe
cies being discovered and that a perplexing multitude of functions
are associated with the different types of RNA. In this introductory
chapter it is essential to explain first why RNA should have so many
diverse functions and to introduce terminology and different types
of regulatory RNA. Specific RNA motifs are distinct parts or seg
ments of the RNA which, due to their primary sequence and struc
ture, are involved in specific interactions of the RNA. Such an inter
action can be within the molecule itself, with other RNA or different
proteins, but the interaction requires exactly this part of the RNA
molecule and specific features of its primary sequence and struc
ture. The interaction exerts control on the RNA molecule, for ex
ample a step in catalysis, the localization of the RNA, the stability of
the molecule against nuclease digestion if it is a nuclease target, or
the speed or start of protein translation from the RNA molecule.
Thus RNA motifs exert control functions on the RNA molecule and
in this sense represent regulatory RNA segments. The whole RNA
molecule containing the RNA motif often becomes a regulatory
molecule due to the interaction mediated by the motif, for instance
as a developmental regulatory molecule, a cellular localization fac
tor, a component directing RNA processing, or a mediator of meta
bolic control. RNA motifs are thus central to any regulation, pattern
formation, catalysis or ribonucleoprotein interactions mediated by
RNAY The specialist may quickly pass over the general introduc
tion to the following chapters. Chapter 2 gives a summary of the
different regulatory RNA types, including examples of specific types,
a summary table and a detailed compilation (which was only updated
Regulatory RNA, by Thomas Dandekar and Kishor Sharma. © 1998 Springer-Vedag
and R.G. Landes Company.