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Epigenetics

(Cold Spring Harbor Symposia on Quantitative Biology LXIX)

Book Series:  Cold Spring Harbor Symposia on Quantitative Biology
Subject Area(s):  Molecular BiologyGenetics

Edited by Bruce Stillman, Cold Spring Harbor Laboratory; David Stewart, Cold Spring Harbor Laboratory

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© 2004 • 532 pp., illus., index

Paperback • $126 63.00 (click here to price in UK Pounds)
ISBN  978-087969731-0
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Description

The importance of epigenetic regulation of gene expression, particularly in higher organisms, is now clear and the 2004 Cold Spring Harbor Annual Symposium provided many new examples as well as insights into the underlying mechanisms. The resulting volume—with over 60 papers from experts across the field—covers various aspects of nuclear organization and dynamics; genomic imprinting, chromosomal inactivation, and other examples of gene silencing; the histone and DNA modifications associated with these conditions; and the roles of RNA and protein regulators in establishing and maintaining these states.

Contents

Symposium Participants
Foreword
Epigenetic Reprogramming and Genomic Imprinting
Mechanism of Mouse Germ Cell Specification: A Genetic Program Regulating Epigenetic Reprogramming
M.A. Surani, K. Ancelin, P. Hajkova, U.C. Lange, B. Payer, P. Western, and M. Saitou
Epigenetic Mechanisms in Early Mammalian Development
D. Solter, T. Hiiragi, A.V. Evsikov, J. Moyer, W.N. de Vries, A.E. Peaston, and B.B. Knowles
Nuclear Cloning, Epigenetic Reprogramming, and Cellular Differentiation
R. Jaenisch, K. Hochedlinger, R. Blelloch, Y. Yamada, K. Baldwin, and K. Eggan
Chromosome Loops, Insulators, and Histone Methylation: New Insights into Regulation of Imprinting in Clusters
W. Reik, A. Murrell, A. Lewis, K. Mitsuya, D. Umlauf, W. Dean, M. Higgins, and R. Feil
Genomic Imprinting: Antagonistic Mechanisms in the Germ Line and Early Embryo
A.M. Fedoriw, N.I. Engel, and M.S. Bartolomei
Drosophila Su(Hw) Regulates an Evolutionarily Conserved Silencer from the Mouse H19 Imprinting Control Region
S. Schoenfelder and R. Paro
The Air Noncoding RNA: An Imprinted cis–silencing Transcript
G. Braidotti, T. Baubec, F. Pauler, C. Seidl, O. Smrzka, S. Stricker, I. Yotova, and D.P. Barlow
The (Dual) Origin of Epigenetics
D. Haig
Chromosome Inactivation
Sex and X–Chromosome–wide Repression in Caenorhabditis elegans
B.J. Meyer, P. McDonel, G. Csankovszki, and E. Ralston
Targeting Dosage Compensation to the X Chromosome of Drosophila Males
H. Oh, X. Bai, Y. Park, J.R. Bone, and M.I. Kuroda
Mammalian X–Chromosome Inactivation: An Epigenetics Paradigm
E. Heard, J. Chaumeil, O. Masui, and I. Okamoto
A Continuity of X–Chromosome Silence from Gamete to Zygote
K.D. Huynh and J.T. Lee
DNA Methylation
Reading the DNA Methylation Signal
A. Bird and D. Macleod
Genome Defense and DNA Methylation in Neurospora
E.U. Selker
Role of De Novo DNA Methyltransferases in Initiation of Genomic Imprinting and X–Chromosome Inactivation
M. Kaneda, T. Sado, K. Hata, M. Okano, N. Tsujimoto, E. Li, and H. Sasaki
Gene Repression Paradigms in Animal Cells
L. Lande–Diner, J. Zhang, T. Hashimshony, A. Goren, I. Keshet, and H. Cedar
Control of Development and Transposon Movement by DNA Methylation in Arabidopsis thaliana
T. Kakutani, M. Kato, T. Kinoshita, and A. Miura
DNA Methylation of the Endogenous PAI Genes in Arabidopsis
J. Bender
Induced and Natural Epigenetic Variation
H. Yi, N.C. Riddle, T.L. Stokes, H.–R. Woo, and E.J. Richards
Histone Modification and Nucleosome Structure
Linking Covalent Histone Modifications to Epigenetics: The Rigidity and Plasticity of the Marks
Y. Wang, J. Wysocka, J.R. Perlin, L. Leonelli, C.D. Allis, and S.A. Coonrod
Steps Toward Understanding the Inheritance of Repressive Methyl–Lysine Marks in Histones
D. Reinberg, S. Chuikov, P. Farnham, D. Karachentsev, A. Kirmizis, A. Kuzmichev, R. Margueron, K. Nishioka, T.S. Preissner, K. Sarma, C. Abate–Shen, R. Steward, and A. Vaquero
Noncovalent Modification of Chromatin: Different Remodeled Products with Different ATPase Domains
H.–Y. Fan, G.J. Narlikar, and R.E. Kingston
Acetylation of Yeast Histone H4 Lysine 16: A Switch for Protein Interactions in Heterochromatin and Euchromatin
C.B. Millar, S.K. Kurdistani, and M. Grunstein
Histone Deposition Proteins: Links between the DNA Replication Machinery and Epigenetic Gene Silencing
A.A. Franco and P.D. Kaufman
Trilogies of Histone Lysine Methylation as Epigenetic Landmarks of the Eukaryotic Genome
M. Lachner, R. Sengupta, G. Schotta, and T. Jenuwein
Histone H3 Amino–Terminal Tail Phosphorylation and Acetylation: Synergistic or Independent Transcriptional Regulatory Marks?
C.J. Fry, M.A. Shogren–Knaak, and C.L. Peterson
Structural Characterization of Histone H2A Variants
S. Chakravarthy, Y. Bao, V.A. Roberts, D. Tremethick, and K. Luger
Chromatin Structure and Dynamics
Epigenetics, Histone H3 Variants, and the Inheritance of Chromatin States
S. Henikoff, E. McKittrick, and K. Ahmad
Chromatin Boundaries and Chromatin Domains
G. Felsenfeld, B. Burgess–Beusse, C. Farrell, M. Gaszner, R. Ghirlando, S. Huang, C. Jin, M. Litt, F. Magdinier, V. Mutskov, Y. Nakatani, H. Tagami, A. West, and T. Yusufzai
Do Higher–Order Chromatin Structure and Nuclear Reorganization Play a Role in Regulating Hox Gene Expression during Development?
W.A. Bickmore, N.L. Mahy, and S. Chambeyron
SIR1 and the Origin of Epigenetic States in Saccharomyces cerevisiae
L. Pillus and J. Rine
Analyzing Heterochromatin Formation Using Chromosome Four of Drosophila melanogaster
K.A. Haynes, B.A. Leibovitch, S.H. Rangwala, C. Craig, and S.C.R. Elgin
Two Distinct Nucleosome Assembly Pathways: Dependent or Independent of DNA Synthesis Promoted by Histone H3.1 and H3.3 Complexes
Y. Nakatani, D. Ray–Gallet, J.–P. Quivy, H. Tagami, and G. Almouzni
The Chromatin Accessibility Complex: Chromatin Dynamics through Nucleosome Sliding
P.B. Becker
Histone H2B Ubiquitylation and Deubiquitylation in Genomic Regulation
N.C.T. Emre and S.L. Berger
Polycomb and Related Silencing Mechanisms
Polycomb Silencing Mechanisms in Drosophila
Y.B. Schwartz, T.G. Khan, G.I. Dellino, and V. Pirrotta
Mechanism of Polycomb Group Gene Silencing
Y. Zhang, R. Cao, L. Wang, and R.S. Jones
Emerging Roles of Polycomb Silencing in X–Inactivation and Stem Cell Maintenance
I. Muyrers–Chen, I. Hernández–Muñoz, A.H. Lund, M.E. Valk–Lingbeek, P. van der Stoop, E. Boutsma, B. Tolhuis, S.W.M. Bruggeman, P. Taghavi, E. Verhoeven, D. Hulsman, S. Noback, E. Tanger, H. Theunissen, and M. van Lohuizen
Nuclear Organization and Dynamics
The Function of Telomere Clustering in Yeast: The Circe Effect
S.M. Gasser, F. Hediger, A. Taddei, F.R. Neumann, and M.R. Gartenberg
Genetic Instability in Aging Yeast: A Metastable Hyperrecombinational State
M.A. McMurray and D.E. Gottschling
Restructuring the Genome in Response to Adaptive Challenge: McClintock’s Bold Conjecture Revisited
R.A. Jorgensen
Poetry of b1 Paramutation: cis– and trans–Chromatin Communication
V.L. Chandler
Heterochromatin and Transposon Silencing RNA
Silencing Pathways in Plants
A.J. Herr and D.C. Baulcombe
Transposons, Tandem Repeats, and the Silencing of Imprinted Genes
R. Martienssen, Z. Lippman, B. May, and M. Vaughn
Transposon Silencing and Imprint Establishment in Mammalian Germ Cells
T.H. Bestor and D. Bourc’his
RNA Interference, Heterochromatin, and Centromere Function
R.C. Allshire
RNA Interference, Transposon Silencing, and Cosuppression in the Caenorhabditis elegans Germ Line: Similarities and Differences
V.J.P. Robert, N.L. Vastenhouw, and R.H.A. Plasterk
RNA Interference and Related Mechanisms
Plant RNA Interference in Vitro
C. Matranga and P.D. Zamore
A Conserved microRNA Signal Specifies Leaf Polarity
M.C.P. Timmermans, M.T. Juarez, and T.L. Phelps–Durr
RNA Interference and Epigenetic Control of Heterochromatin Assembly in Fission Yeast
H. Cam and S.I.S. Grewal
Regulation of Caenorhabditis elegans RNA Interference by the daf–2 Insulin Stress and Longevity Signaling Pathway
D. Wang and G. Ruvkun
Interrelationship of RNA Interference and Transcriptional Gene Silencing in Drosophila
M. Pal–Bhadra, U. Bhadra, and J.A. Birchler
Functional Identification of Cancer–relevant Genes through Large–Scale RNA Interference Screens in Mammalian Cells
T.R. Brummelkamp, K. Berns, E.M. Hijmans, J. Mullenders, A. Fabius, M. Heimerikx, A. Velds, R.M. Kerkhoven, M. Madiredjo, R. Bernards, and R.L. Beijersbergen
Epigenetic Regulation of Phenotypes
The New Field of Epigenomics: Implications for Cancer and Other Common Disease Research
H.T. Bjornsson, H. Cui, D. Gius, M.D. Fallin, and A.P. Feinberg
Epigenetic Regulation in the Control of Flowering
J. Mylne, T. Greb, C. Lister, and C. Dean
Transposons and Tandem Repeats Are Not Involved in the Control of Genomic Imprinting at the MEDEA Locus in Arabidopsis
C. Spillane, C. Baroux, J.–M. Escobar–Restrepo, D.R. Page, S. Laoueille, and U. Grossniklaus
Toward Molecular Understanding of Polar Overdominance at the Ovine Callipyge Locus
M. Georges, C. Charlier, M. Smit, E. Davis, T. Shay, X. Tordoir, H. Takeda, F. Caiment, and N. Cockett
Dscam–mediated Self– versus Non–Self–Recognition by Individual Neurons
G. Neves and A. Chess
Prions of Yeast Are Genes Made of Protein: Amyloids and Enzymes
R.B. Wickner, H.K. Edskes, E.D. Ross, M.M. Pierce, F. Shewmaker, U. Baxa, and A. Brachmann
A Possible Epigenetic Mechanism for the Persistence of Memory
K. Si, S. Lindquist, and E. Kandel
An Epigenetic Hypothesis for Human Brain Laterality, Handedness, and Psychosis Development
A.J.S. Klar
Summary: Epigenetics–from Phenomenon to Field
D. Gottschling
Author Index
Subject Index

Related Titles


Epigenetics [Hardcover]

Epigenetics [Hardcover]