Histone Deacetylases: Transcriptional Regulation and Other Cellular Functions

349 Pages·2006·7.767 MB·English

by  Dominique Meunier PhD, Christian Seiser PhD (auth.), Eric Verdin MD (eds.)

H D
ISTONE EACETYLASES
C D D
ANCER RUG ISCOVERY
D
AND EVELOPMENT
B A. T , S E
EVERLY EICHER ERIES DITOR
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H
ISTONE
D
EACETY LASES
T R
RANSCRIPTIONAL EGULATION
O C F
AND THER ELLULAR UNCTIONS
Edited by
E V ,
RIC ERDIN MD
Gladstone Institute of Virology and Immunology
University of California, San Francisco, CA
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Library of Congress Cataloging-in-Publication Data
Histone deacetylases : transcriptional regulation and other cellular functions / edited by Eric Verdin.
p. ; cm. -- (Cancer drug discovery and development)
Includes bibliographical references and index.
ISBN 1-58829-499-4 (alk. paper)
1. Histone deacetylase. 2. Cell cycle. 3. Enzymes. 4. Cancer --Chemotherapy. I. Verdin, Eric. II. Series.
[DNLM: 1. Histone Deacetylases--physiology. 2. Cell Cycle--drug effects. 3. Enzyme Repression--
physiology. 4. Histone Deacetylases--antagonists & inhibitors. 5. Neoplasms--drug therapy. 6. Sirtuins--
physiology. QU 136 H673 2006]
QP552.H5H55 2006
616.99'4061--dc22
2005031537
P
REFACE
Forty years ago, Vince Allfrey discovered the reversible acetylation of histone
proteins and proposed that this posttranslational modification could regulate gene
expression(1). The role of histone acetylation in transcriptional regulation remained
controversial until 1996, when two papers reported the identification of the first
acetyltransferase, GCN5 (2) and the first histone deacetylase, HDAC1 (3). The
realization that these enzymes were homologous to previously identified yeast
transcriptional regulators established histone acetylation as a key regulatory
mechanism for gene expression.
These discoveries have triggered a wave of interest in histone posttranslational
modifications and have led to the discovery of 18 potential human histone
deacetylases in the past eight years. Human histone deacetylases are divided into
three families, Class I (HDAC1, -2, -3, and -8) and Class II HDACs (HDAC4, -5,
-6, -7, 9, -10, and -11), are homologous to the yeast histone deacetylases Rpd3 and
Hda1, respectively, and share some degree of sequence homology. In contrast, the
Class III histone deacetylases are homologous to the yeast protein Sir2 and use NAD
as a cofactor. The human class III HDACs are called sirtuins (SIRT1–7). In many
cases, these deacetylases target nonhistone proteins for deacetylation, suggesting
that their biological activities go beyond gene regulation. Despite the youth of this
research field, the first inhibitors of histone deacetylases are in clinical trials as novel
anticancer agents.
The purpose of Histone Deacetylases: Transcriptional Regulation and Other
Cellular Functions is to summarize this rapidly evolving field. Much has been
learned about these proteins, including the identification of the enzymes, the
elucidation of their enzymatic mechanisms of action, and the identification of their
substrates and partners. Structures have been solved for a number of enzymes, alone
or in complex with small-molecule inhibitors. Several HDAC genes have been
knocked out in mice and their biological roles have been defined. Despite these
impressive advances, our knowledge is still fragmentary and much remains to be
done.
We hope that this book will serve as a landmark survey of what has been
accomplished in these first eight years. We also hope that we have successfully
outlined for our readers a clear agenda of what needs to be done in the next few years
to define fully the role of HDACs in biology and in disease.
Eric Verdin, MD
1. Allfrey VG, Faulkner R, Mirsky AE. Acetylation and methylation of histones and
their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci USA
1964;51:786–794.
v
vi Preface
2. Brownell JE, Zhou J, Ranalli T, et al. Tetrahymena histone acetyltransferase A:
a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell
1996;84:843–851.
3. Taunton J, Hassig CA, Schreiber SL. A mammalian histone deacetylase related to
the yeast transcriptional regulator Rpd3p. Science 1996;272:408–411.
C
ONTENTS
Preface...............................................................................................................v
Contributors......................................................................................................ix
Color Plates......................................................................................................xi
I. CLASS I HISTONE DEACETYLASES
1 Histone Deacetylase 1
Dominique Meunier and Christian Seiser............................................3
2 Biochemistry of Multiprotein HDAC Complexes
Alejandro Vaquero, Michael Scher, and Danny Reinberg................23
3 The Biology of HDAC3
Edward Seto ..........................................................................................61
4 The Biology of HDAC8, a Unique Class I Histone Deacetylase
David Waltregny and Vincent Castronovo..........................................87
II. CLASS II HISTONE DEACETYLASES
5 Regulation of Muscle Gene Expression by Histone Deacetylases
Timothy A. McKinsey and Eric N. Olson..........................................107
6 The Class IIa Histone Deacetylases: Functions and Regulation
Herbert G. Kasler and Eric Verdin....................................................129
7 Histone Deacetylases in the Response to Misfolded Proteins
J. Andrew McKee and Tso-Pang Yao................................................165
III. CLASS III HISTONE DEACETYLASES
8 Evolution of Sirtuins From Archaea to Vertebrates
Roy A. Frye .........................................................................................183
+
9 Structure of the Sir2 Family of NAD -Dependent Histone/Protein
Deacetylases
Kehao Zhao and Ronen Marmorstein...............................................203
10 The Enzymology of SIR2 Proteins
Margie T. Borra and John M. Denu.................................................219
11 The Class III Protein Deacetylases: Homologs of Yeast Sir2p
Bjoern Schwer, Brian J. North, Nidhi Ahuja, Brett Marshall,
and Eric Verdin..............................................................................237
vii
viii Contents
IV. HISTONE DEACETYLASE INHIBITORS
12 HDAC Inhibitors: Discovery, Development, and Clinical Impacts
Akihiro Ito, Norikazu Nishino, and Minoru Yoshida......................271
13 Cell Cycle Targets of Histone Deacetylase Inhibitors
Brian Gabrielli....................................................................................299
14 HDAC Inhibitors: An Emerging Anticancer Therapeutic Strategy
Paul Kwon, Meier Hsu, Dalia Cohen, and Peter Atadja .................315
Index..............................................................................................................333
C
ONTRIBUTORS
NIDHI AHUJA,PhD(cid:129)Gladstone Institutes, University of California,
San Francisco, CA
PETER ATADJA,PhD(cid:129)Department of Oncology, Novartis Institutes
for Biomedical Research, Cambridge, MA
MARGIE T. BORRA,PhD(cid:129)Department of Biomolecular Chemistry, University
of Wisconsin, Madison, Madison, WI
VINCENT CASTRONOVO,MD,PhD(cid:129)Biologie Générale et Cellulaire, Labo
de Recherche sur les Métastases, University of Liège, Liège, Belgium
DALIA COHEN,PhD(cid:129)Department of Functional Genomics, Novartis Institutes
for Biomedical Research, Cambridge, MA
JOHN M. DENU,PhD(cid:129)Department of Biomolecular Chemistry, University
of Wisconsin, Madison, Madison, WI
ROY A. FRYE,MD,PhD(cid:129)Department of Pathology, University of Pittsburgh,
Pittsburgh, PA
BRIAN GABRIELLI,PhD(cid:129)Epithelial Pathobiology Group, Centre
for Immunology and Cancer Research, University of Queensland
Department of Medicine, Princess Alexandra Hospital, Brisbane,
Queensland, Australia
MEIER HSU(cid:129)Department of Oncology, Novartis Institutes for Biomedical
Research, Cambridge, MA
AKIHIRO ITO,PhD(cid:129)Chemical Genetics Laboratory, RIKEN, Saitama, Japan
HERBERT G. KASLER,PhD(cid:129)Gladstone Institute of Virology and Immunology,
University of California, San Francisco, CA
PAUL KWON(cid:129)Department of Oncology, Novartis Institutes for Biomedical
Research, Cambridge, MA
RONEN MARMORSTEIN,PhD(cid:129)Professor, Gene Expression and Regulation
Program, The Wistar Institute, Philadelphia, PA
BRETT MARSHALL(cid:129)Gladstone Institute of Virology and Immunology,
University of California, San Francisco, CA
J. ANDREW MCKEE,MD(cid:129)Department of Pharmacology and Cancer Biology,
Duke University, Durham, NC
TIMOTHY A. MCKINSEY,PhD(cid:129)Myogen, Inc, Westminster, CO
ix