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Takashi Ohyama
Konan University

About this book

The 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 constitutes 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 packaging 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.

Table of contents

PART I. MULTIFARIOUS DNA STRUCTURES FOUND IN GENOMES

1. DNA: Alternative Conformations and Biology
Vladimir N. Potaman and Richard R. Sinden

2. Sequence-Dependent Variability of B-DNA: An Update on Bending
and Curvature
Victor B. Zhurkin, Michael Y. Tolstorukov, Fei Xu, Andrew V. Colasanti
and Wilma K. Olson

PART II. INTRINSIC DNA CURVATURE AND TRANSCRIPTION

3. Curved DNA and Prokaryotic Promoters: A Mechanism for Activation
of Transcription
Munehiko Asayama and Takashi Ohyama

4. Repression of Transcription by Curved DNA and Nucleoid Protein H-NS:
A Mode of Bacterial Gene Regulation
Cynthia L. Pon, Stefano Stella and Claudio O. Gualerzi

5. Curved DNA and Transcription in Eukaryotes
Takashi Ohyama

6. Putative Roles of kin17, a Mammalian Protein Binding Curved DNA,
in Transcription
Jaime F. Angulo, Philippe Mauffrey, Ghislaine Pinon-Lataillade, Laurent Miccoli
and Denis S.F. Biard

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
Alan Herbert

8. Do DNA Triple Helices or Quadruplexes Have a Role in Transcription?
Michael W. Van Dyke

9. Nucleic Acid Structures and the Transcription Defects in Fragile X Syndrome and Friedreich’s Ataxia
Karen Usdin

10. Possible Roles of DNA Supercoiling in Transcription
Susumu Hirose and Kuniharu Matsumoto

PART IV. DNA-BENDING PROTEINS: ARCHITECTURAL REGULATION
OF TRANSCRIPTION

11. Gene Regulation by HMGA and HMGB Chromosomal Proteins and Related Architectural DNA-Binding Proteins
Andrew A. Travers

12. Molecular Mechanisms of Male Sex Determination: The Enigma of SRY
Michael A. Weiss

PART V. CHROMATIN INFRASTRUCTURE IN TRANSCRIPTION:
ROLES OF DNA CONFORMATION AND PROPERTIES

13. The Role of Unusual DNA Structures in Chromatin Organization
for Transcription
Takashi Ohyama

14. DNA Bendability and Nucleosome Positioning in Transcriptional Regulation
Mensur Dlaki, David W. Ussery and Søren Brunak