DNA Conformation and Transcription

214 Pages·2005·6.744 MB·English

by  Takashi Ohyama Ph.D. (auth.)

MOLECULAR BIOLOGY
INTELUGENCE
UNIT
DNA Conformation
and Transcription
Takashi Ohyama, Ph.D.
Department of Biology
Faculty of Science and Engineering
Konan University
Kobe, Japan
LANDES BIOSCIENCE / EUREKAH.COM SPRINGER SCIENCE+BUSINESS MEDIA
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U.S.A. U.SA
DNA CONFORMATION AND TRANSCRIPTION
Molecular Biology Intelligence Unit
Landes Bioscience / Eurekah.com
Springer Science+Business Media, Inc.
ISBN: 0-387-25579-6 Printed on acid-free paper.
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Library of Congress Cataloging-in-Publication Data
DNA conformation and transcription / [edited by] Takashi Ohyama.
p. ; cm. ~ (Molecular biology intelligence unit)
Includes bibliographical references and index.
ISBN 0-387-25579-6
1. DNA~Conformation. 2. Genetic transcription. I. Ohyama,
Takashi. II. Series: Molecular biology intelligence unit
(Unnumbered)
[DNLM: 1. DNA~chemistry. 2. DNA-metabolism. 3. Nucleic
Acid Conformation. 4. Transcription, Genetic. QU 58.5 D62907
2005]
QP624.5.S78D58 2005
6ll'.018166--dc22
2005012636
CONTENTS
Preface xi
Parti
Multifarious DNA Structures Found in Genomes
1. DNA: Alternative Conformations and Biology 3
Vladimir N. Potaman and Richard R Sinden
B-DNAandA-DNA 3
DNA Supercoiling 6
Supercoil-Induced DNA Structures and Their Biological Roles 7
Slipped-Strand DNA 12
DNA Unwinding Elements 13
2. Sequence-Dependent Variability of B-DNA:
An Update on Bending and Curvature 18
Victor B. Zhurkin, Michael Y. TolstorukoVy Fei Xu,
Andrew V Colasanti and Wilma K. Olson
B-DNA Family of Forms 19
Sequence-Dependent Anisotropic Bending of DNA 19
A-Tract Curvature: AA-Wedge, Purine-Clash,
and Junction Models 20
Non-A-Tract Model 23
High-Resolution NMR Structures of A-Tract DNA 24
Modeling of A-Tract Curvature Based on NMR and X-Ray Data 27
Unresolved Problems: Sugar Switching
and Overall DNA Flexibility 28
Genome-Wide A-Tract Distribution in Bacteria 30
Part II
Intrinsic DNA Curvature and Transcription
3. Curved DNA and Prokaryotic Promoters:
A Mechanism for Activation of Transcription 37
Munehiko Asayama and Takashi Ohyama
The Shape of Curved DNA 38
Mapping Curved DNA Loci 39
Role of the Curved DNA 42
Intrinsic DNA Curvature and Transcription-Factor
Induced DNA Bend AG
4. Repression of Transcription by Curved DNA
and Nucleoid Protein H-NS: A Mode of Bacterial Gene Regulation .... 52
Cynthia L Pon, Stefano Stella and Claudio O. Gualerzi
Relationship between Function and Three-Dimensional
and Quaternary Structure of H-NS 53
Architectural Role of H-NS 56
DNA Bending and H-NS Activity 57
Transcriptional Regulation by H-NS and Thermosensing
through Curved DNA 58
5. Curved DNA and Transcription in Eukaryotes (iG
Takashi Ohyama
Intrinsic DNA Bends in Control Regions of Transcription GG
Role of Intrinsic DNA Curvature in Transcription 70
6. Putative Roles of kin 17, a Mammalian Protein Binding
Curved DNA, in Transcription 75
Jaime F. Angulo, Philippe Maujfrey, Ghislaine Pinon-Latailladcj
Laurent Miccoli and Denis S.F. Biard
Identification of kinl7 Protein 75
Molecular Characterization of kinl7 Protein 76
Evidence for the Participation of kin 17 Protein in Transcription 78
Evidence Pointing to a Role of kin 17 Protein in DNA Replication 82
Part III
Implied Roles of Left-Handed Z-DNA,
Triplex DNA, DNA Supercoiling,
and Miscellaneous Alternative Conformations
of DNA in Transcription
7. Roles for Z-DNA and Double-Stranded RNA in Transcription:
Encoding Genetic Information by Shape Rather than by Sequence 93
Alan Herbert
Formation of Z-DNA 94
Potential Roles for the Z-DNA Conformation Due
to Its Physical Presence 94
Protein Recognition of the Z-DNA Conformation 95
The Za Fold 95
The Za Family of Z-DNA Binding Domains 96
Other Z-DNA Binding Motifs 98
Potential Roles for the Z-DNA Conformation Due
to Protein Recognition 98
8. Do DNA Triple Helices or Quadruplexes Have a Role
in Transcription? 105
Michael W. Van Dyke
DNA Triplexes 105
DNA Quadruplexes 107
Multiplexes and Transcription 108
Intermolecular Triplexes and Transcription 109
Intramolecular Triplexes and Transcription Ill
Quadruplexes and Transcription 118
9. Nucleic Acid Structures and the Transcription Defects
in Fragile X Syndrome and Friedreich's Ataxia 127
Karen Usdin
Unusual Nucleic Acid Structures Are Formed by the FXS
and FRDA Repeats 128
The Potential Biological Significance of These Structures 130
10. Possible Roles of DNA Supercoiiing in Transcription 138
Susumu Hirose and Kuniharu Matsumoto
Prokaryotic Transcription 138
Eukaryotic Transcription 140
Part IV
DNA-Bending Proteins:
Architectural Regulation of Transcription
11. Gene Regulation by HMGA and HMGB Chromosomal Proteins
and Related Architectural DNA-Binding Proteins 147
Andrew A. Travers
Architectural DNA Binding Proteins 147
Principles of Transcription Factor Induced Bending 148
Biological Functions of DNA Bending 149
HMGA Proteins 150
HMGB Proteins 152
12. Molecular Mechanisms of Male Sex Determination:
The Enigma of SRY 159
Michael A. Weiss
Structure of the HMG Box and Protein-DNA Complexes 160
Insights from Comparison of Human and Murine SRY 162
The Biochemical Basis for the Genetic Function of 5ry 165
PartV
Chromatin Infirastructure in Transcription:
Roles of DNA Conformation and Properties
13. The Role of Unusual DNA Structures
in Chromatin Organization for Transcription 177
Takashi Ohyama
Curved DNA and DNA Packaging in Chromatin 178
Poly(dA*dT) Sequences and Nucleosome Positioning 181
Chromatin and Z-DNA, Triple-Stranded DNA,
and Cruciform DNA 183
14. DNA Bendability and Nucleosome Positioning
in Transcriptional Regulation 189
Mensur Dlakic, David W. Ussery and Seven Brunak
Comparison of Nucleosomal DNA
with B-DNA Oligonucleotides 190
DNA Bending and Flexibility Are Utilized
for Nucleosome Positioning 193
Preference of Nucleosomal Positioning in Exon and Intron DNA 193
Nucleosome Positioning and Transcriptional Regulation 197
Index 203
EDITOR
Takashi Ohyama
Department of Biology
Faculty of Science and Engineering
Konan University
Kobe, Japan
Email: [email protected]
Chapters 3y5y 13
^CONTRIBUTORS^
Jaime F. Angulo Soren Brunak
Laboratoire de Genetique Center for Biological Sequence Analysis
de la Radiosensibilite Biocentrum-DTU
D^partement de Radiobiologie The Technical University of Denmark
et de Radiopathologie Lyngby, Denmark
Direction des Sciences du Vivant Email: [email protected]
Commissariat a TEnergie Atomique Chapter 14
Centre d'Etudes de Fontenay-Aux-Roses
Fontenay-Aux-Roses, France Andrew V. Colasanti
Email: [email protected] Wright-Rieman Laboratories
Chapter 6 Rutgers University
Piscataway, New Jersey, U.S.A.
Munehiko Asayama Email: [email protected]
Laboratory of Molecular Genetics Chapter 2
School of Agriculture
Ibaraki University Mensur Dlakic
Ibaraki, Japan Department oicf Microbiology
Email: [email protected] Montana State University
Chapter 3 Bozeman, Montana, U.S.A.
Email: [email protected]
Denis S.F. Biard Chapter 14
Laboratoire de Genetique
de la Radiosensibilite Claudio O. Gualerzi
Departement de Radiobiologie Department of Biology MCA
et de Radiopathologie University of Camerino
Direction des Sciences du Vivant Camerino (MC), Italy
Commissariat a TEnergie Atomique Email: [email protected]
Centre d*Etudes de Fontenay-Aux-Roses Chapter 4
Fontenay-Aux-Roses, France
Email: [email protected] Alan Herbert
Chapter 6 Framingham Heart Study Genetics
Laboratory
Department of Neurology
Boston University School of Medicine
Boston, Massachusetts, U.S.A.
Email: [email protected]
Chapter 7
Susumu Hirose Ghislaine Pinon-Lataillade
Department of Developmental Genetics Laboratoire de Genetique
National Institute of Genetics de la Radiosensibilite
Mishima, Japan Departement de Radiobiologie
Email: [email protected] et de Radiopathologie
Chapter 10 Direction des Sciences du Vivant
Commissariat a I'Energie Atomique
Kuniharu Matsumoto Centre d'Etudes de Fontenay-Aux-Roses
Department of Developmental Genetics Fontenay-Aux-Roses, France
National Institute of Genetics Email: [email protected]
Mishima, Japan Chapter 6
Email: [email protected]
Chapter 10 Cynthia L. Pon
Department of Biology MCA
Philippe MaufFrey University of Camerino
Laboratoire de Genetique Camerino (MC), Italy
de la Radiosensibilite Email: [email protected]
Departement de Radiobiologie Chapter 4
et de Radiopathologie
Direction des Sciences du Vivant Vladimir N. Potaman
Commissariat a TEnergie Atomique Center for Genome Research
Centre d Etudes de Fontenay-Aux-Roses Institute of Biosciences and Technology
Fontenay-Aux-Roses, France Texas A&M University System Health
Email: [email protected] Sciences Center
Chapter 6 Houston, Texas, U.S.A.
Email: [email protected]
Laurent Miccoli Chapter 1
Laboratoire de Genetique
de la Radiosensibilite Richard R. Sinden
Departement de Radiobiologie Laboratory of DNA Structure
et de Radiopathologie and Mutagenesis
Direction des Sciences du Vivant Center for Genome Research
Commissariat a TEnergie Atomique Institute of Biosciences and Technology
Centre d^Etudes de Fontenay-Aux-Roses Texas A&M University System Health
Fontenay-Aux-Roses, France Sciences Center
Email: [email protected] Houston, Texas, U.S.A.
Chapter 6 Email: [email protected]
Chapter 1
WilmaK. Olson
Wright-Rieman Laboratories Stefano Stella
Rutgers University Department of Biology MCA
Piscataway, New Jersey, U.S.A. University of Camerino
Email: [email protected] Camerino (MC), Italy
Chapter 2 Email: [email protected]
Chapter 4
Michael Y. Tolstorukov Michael A. Weiss
Laboratory of Experimental Department of Biochemistry
and Computational Biology Case Western Reserve University
National Cancer Institute, NIH Cleveland, Ohio, U.S.A
Bethesda, Maryland, U.S.A. Email: [email protected]
Email: [email protected] Chapter 12
Chapter 2
FeiXu
Andrew A. Travers Wright-Rieman Laboratories
MRC Laboratory of Molecular Biology Rutgers University
Cambridge, U.K. Piscataway, New Jersey, U.S.A.
Email: [email protected] Email: [email protected]
Chapter 11 Chapter 2
Karen Usdin Victor B. Zhurkin
Genomic Structure and Function Section Laboratory of Experimental
Laboratory of Molecular and Computational Biology
and Cellular Biology National Cancer Institute, NIH
National Institute of Diabetes Bethesda, Maryland, U.S.A,
Digestive and Kidney Diseases Email: [email protected]
National Institutes of Health Chapter 2
Bethesda, Maryland, U.S.A.
Email: [email protected]
Chapter 9
David W. Ussery
Center for Biological Sequence Analysis
Biocentrum-DTU
The Technical University of Denmark
Lyngby, Denmark
Email: [email protected]
Chapter 14
Michael W. Van Dyke
Department of Molecular
and Cellular Oncology
University of Texas M.D. Anderson
Cancer Center
Houston, Texas, U.S.A
Email: [email protected]
Chapter 8
PREFACE
T
he human genome project was virtually completed in 2003, the same
year in which the 50th anniversary of the discovery of the DNA
double helix came around. This project has opened the door to the
genomic era. Nowadays, we have easy access to genome sequence databases
for more than 100 organisms. However, despite such remarkable progress in
genome science, we are still far from a clear understanding of how genomic
DNA is packaged without entanglement into a nucleus, how genes are
wrapped up in chromatin, how chromatin structure is faithfully inherited
from mother to daughter cells, and how the differential expression of genes is
enabled in a given cell type. Exploring and answering these questions consti
tutes one of the next frontiers in the 21st century.
Multifarious DNA structures are found in the genome, i.e., curved
DNA structures found in regions of periodically occurring A-tracts, triplex
structures composed of homopurine/homopyrimidine regions, quadruplex
structures made up of guanine-rich sequences, left-handed DNA helix
(Z-DNA) formed by alternating purine-pyrimidine sequences, cruciform
structures formed by inverted repeats, and so forth. The implication of these
structures for DNA packs^ing and gene expression has long been argued. In
the meantime, much circumstantial evidence and several lines of direct
evidence have been presented, and we are beginning to appreciate how these
structures provide additional structural and functional dimensions to
chromatin organization and gene expression. However, to the best of my
knowledge, there is no book in which the fruits of the studies performed to
date have been compiled, in order to shed light on the roles of DNA
conformation in transcription.
The challenge of this book is to collect these results, and it is intended
to serve as a source of information. The book is not only aimed at specialists,
but also at students and non-specialists who have no prior knowledge of this
field. Contributors from the respective fields describe, in 14 chapters, the
history, up-to-date topics, what has been clarified, and what is still to be
discovered. These chapters are grouped into five closely related parts. Part I
presents fiindamental knowledge on DNA structure, which will simply guide
the reader into the *DNA world'. Readers will see that there are many DNA
structures in genomes besides the DNA described by James D. Watson and
Francis H. C. Crick, which is now called B-form DNA, and will fiirther
understand how these structures are constructed and what possible biological
fiinctions they may have. In Part II, the role of curved DNA is discussed.
Among the multifarious DNA structures, curved DNA has been most widely
and intensively studied in relation to transcriptional regulation. The roles of
this structure in both prokaryotic and eukaryotic transcription are discussed,
and the proteins that bind curved DNA and their functional roles are
described. Part III focuses on the role of Z-DNA, triplex, quadruplex and