Nuclear Organization and Function Cold Spring Harbor Symposia on Quantitative Biology, Volume LXXV

This volume is based on presentations by the world-renowned investigators who gathered at the 75th annual Cold Spring Harbor Symposium on Quantitative Biology to discuss the organization and function of the cell nucleus. It reviews the latest advances in research into nuclear structure, the organization of the genome within the nucleus, and spatiotemporal coordination of nuclear processes. The topics examined include nuclear domains, chromatin organization, transcription and RNA processing, DNA replication, nuclear reprogramming, and epigenetics. Cancer, premature aging syndromes, and other diseases that may be associated with altered nuclear organization are also covered.

Chromatin Modifications and Gene Expression

Drosophila Heat Shock System as a General Model to Investigate Transcriptional Regulation
M.J. Guertin, S.J. Petesch, K.L. Zobek, I.M. Min, and J.T. Lis
Chromatin in the Nuclear Landscape
D.B. Beck, R. Bonasio, S. Kaneko, G. Li, G. Li, R. Margueron, H. Oda, K. Sarma, R.J. Sims III, J. Son, P. Trojer, and D. Reinberg
Cell Signaling and Transcriptional Regulation via Histone Phosphorylation
S.L. Berger
HIRA and Daxx Constitute Two Independent Histone H3.3-Containing Predeposition Complexes
S.J. Elsaesser and C.D. Allis
The INO80 Family of Chromatin-Remodeling Enzymes: Regulators of Histone Variant Dynamics
S. Watanabe and C.L. Peterson
Role of K3K27 Demethylases Jmjd3 and UTX in Transcriptional Regulation
M.R. Hübner and D.L. Spector
Epigenetic Inheritance of Centromeres
S. Henikoff and T. Furuyama
Functional Dissection of Polycomb Repressive Complex 1 Reveals the Importance of a Charged Domain
D.J. Grau, J.M. Antao, and R.E. Kingston
Histone Acetylation and the Maintenance of Chromatin Compaction by Polycomb Repressive Complexes
R. Eskeland, E. Freyer, M. Leeb, A. Wutz, and W.A. Bickmore
Chromatin Boundaries, Insulators, and Long-Range Interactions in the Nucleus
K.E. Giles, H. Gowher, R. Ghirlando, C. Jin, and G. Felsenfeld

Transcription and Beyond

Nuclear Origins of Cell-to-Cell Variability
Z. Waks and P.A. Silver
The Role of Cotranscriptional Histone Methylations
S. Buratowski and T. Kim
Chromatin and Alternative Splicing
M. Alló, I.E. Schor, M.J. Muñoz, M. de la Mata,E. Agirre, J. Valcárcel, E. Eyras, and A.R. Kornblihtt
Nuclear Physics: Quantitative Single-Cell Approaches to Nuclear Organization and Gene Expression
T. Lionnet, B. Wu, D. Grünwald, R.H. Singer, and D.R. Larson
CBP80-Promoted mRNP Rearrangements during the Pioneer Round of Translation, Nonsense-Mediated mRNA Decay, and Thereafter
L.E. Maquat, J. Hwang, H. Sato, and Y. Tang

DNA Replication and Genome Integrity

The Many Faces of Redundancy in DNA Replication Control
J.F.X. Diffley
Space and Time in the Nucleus: Developmental Control of Replication Timing and Chromosome Architecture
D.M. Gilbert, S.-I. Takebayashi, T. Ryba, J. Lu, B.D. Pope, K.A. Wilson, and I. Hiratani
Heterochromatin at Mouse Pericentromeres: A Model for De Novo Heterochromatin Formation and Duplication during Replication
C. Maison, J.-P. Quivy, A.V. Probst, and G. Almouzni
How Shelterin Solves the Telomere End-Protection Problem
T. de Lange
The Smc5/6 Complex: More than Repair?
A. Kegel and C. Sjögren

Reprogramming and Differentiation

Efficiencies and Mechanisms of Nuclear Reprogramming
V. Pasque, K. Miyamoto, and J.B. Gurdon
Gene Targeting in Human Pluripotent Cells
D. Hockemeyer and R. Jaenisch
Epigenetic Reprogramming of Mouse Germ Cells toward Totipotency
M.A. Surani and P. Hajkova
Nuclear Mobility and Mitotic Chromosome Binding: Similarities between Pioneer Transcription Factor FoxA and Linker Histone H1
K.S. Zaret, J.M. Caravaca, A. Tulin, and T. Sekiya
Connecting Transcriptional Control to Chromosome Structure and Human Disease
J.J. Newman and R.A. Young
Transcription Factors for the Modulation of Pluripotency and Reprogramming
J.-C.D. Heng, Y.L. Orlov, and H.-H. Ng
Changes in Chromatin Fiber Density as a Marker for Pluripotency
E. Fussner, K. Ahmed, H. Dehghani, M. Strauss, and D.P. Bazett-Jones
Cancer Epigenetics: From Disruption of Differentiation Programs to the Emergence of Cancer Stem Cells
P. Scaffidi and T. Misteli

Heterochromatin Formation and Gene Silencing

Assembly and Functions of Heterochromatin in the Fission Yeast Genome
O. Aygün and S.I.S. Grewal
Germline Reprogramming of Heterochromatin in Plants
K.M. Creasey and R.A. Martienssen
On the Connection between RNAi and Heterochromatin at Centromeres
E. Lejeune, E.H. Bayne, and R.C. Allshire
Evolutionary History of Plant Multisubunit RNA Polymerases IV and V: Subunit Origins via Genome-Wide and Segmental Gene Duplications, Retrotransposition, and Lineage-Specific Subfunctionalization
S.L. Tucker, J. Reece, T.R. Ream, and C.S. Pikaard
Transcriptional Interference and Gene Orientation in Yeast: Noncoding RNA Connections
M. Gullerova and N.J. Proudfoot

Nuclear Bodies and RNA Biology

Cajal Bodies and Histone Locus Bodies in Drosophila and Xenopus
Z.F. Nizami, S. Deryusheva, and J.G. Gall
Down-Regulation of a Host microRNA by a Viral Noncoding RNA
D. Cazalla and J.A. Steitz
Long Noncoding RNAs as Enhancers of Gene Expression
U.A. &Ostrike;rom, T. Derrien, R. Guigo, and R. Shiekhattar
Chromatin Structure and Nuclear Organization Dynamics during X-Chromosome Inactivation
E.P. Nora and E. Heard
XIST RNA and Architecture of the Inactive X Chromosome: Implications for the Repeat Genome
L.L. Hall and J.B. Lawrence
Noncoding Transcripts in Sense and Antisense Orientation Regulate the Epigenetic State of Ribosomal RNA Genes
H. Bierhoff, K. Schmitz, F. Maass, J. Ye, and I. Grummt
Genetic Analysis of Nuclear Bodies: From Nondeterministic Chaos to Deterministic Order
T.K. Rajendra, K. Praveen, and A.G. Matera

Chromosome Structure and Mitosis

Splitting the Nucleus: What's Wrong with the Tripartite Ring Model?
K. Nasmyth and R.A. Oliveira
Physical Linkages between Sister Chromatids and Their Removal during Yeast Chromosome Segregation
J. Baxter and L. Aragón
Molecular Structures and Interactions in the Yeast Kinetochore
U.-S. Cho, K.D. Corbett, J. Al-Bassam, J.J Bellizzi III, P. De Wulf, C.W. Espelin, J.J. Miranda, K. Simons, R.R. Wei, P.K. Sorger, and S.C. Harrison
Centromere Identity, Function, and Epigenetic Propagation across Cell Divisions
B.E. Black, L.E.T. Jansen, D.R. Foltz, and D.W. Cleveland
Temporal and Spatial Regulation of Targeting Aurora B to the Inner Centromere
Y. Watanabe
The Life Cycle of Centrioles
E. Hatch and T. Stearns
Proteomics of Isolated Mitotic Chromosomes Identifies the Kinetochore Protein Ska3/Rama1
S. Ohta, J.-C. Bukowski-Wills, L. Wood, F. de Lima Alves, Z. Chen, J. Rappsilber, and W.C. Earnshaw
New Insight into the Mitotic Chromosome Structure: Irregular Folding of Nucleosome Fibers Without 30-nm Chromatin Structure
K. Maeshima, S. Hihara, and H. Takata
Thoughts on Aneuploidy
E.M. Torres, B.R. Williams, Y.-C. Tang, and A. Amon

Chromatin Structure and Organization

Insights into Interphase Large-Scale Chromatin Structure from Analysis of Engineered Chromosome Regions
A.S. Belmont, Y. Hu, P.B. Sinclair, W. Wu, Q. Bian, and I. Kireev
Chromatin Folding: From Linear Chromosomes to the 4D Nucleus
T. Cheutin, F. Bantignies, B. Leblanc, and G. Cavalli
Functional Nuclear Organization of Transcription and DNA Replication: A Topographical Marriage between Chromatin Domains and the Interchromatin Compartment
Y. Markaki, M. Gunkel, L. Schermelleh, S. Beichmanis, J. Neumann, M. Heidemann, H. Leonhardt, D. Eick, C. Cremer, and T. Cremer
Window into the Complexities of Chromosome Interactomes
A. Göndör, A. Fernandez Woodbridge, C. Shi, E. Aurell, M. Imreh, and R. Ohlsson
Transcription Factories and Nuclear Organization of the Genome
C.H. Eskiw, N.F. Cope, I. Clay, S. Schoenfelder, T. Nagano, and P. Fraser
Role of Nuclear Architecture in Epigenetic Alterations in Cancer
H.P. Easwaran and S.B. Baylin

Nuclear Periphery

Role of the Nuclear Lamina in Genome Organization and Gene Expression
D. Peric-Hupkes and B. van Steensel
Nuclear Lamins in Cell Regulation and Disease
T. Shimi, V. Butin-Israeli, S.A. Adam, and R.D. Goldman
Lamina-Independent Lamins in the Nuclear Interior Serve Important Functions
T. Dechat, K. Gesson, and R. Foisner
Three-Dimensional Organization of Chromatids by Nuclear EnvelopeAssociated Structures
G. Blobel
Repetitive Transgenes in C. elegans Accumulate Heterochromatic Marks and Are Sequestered at the Nuclear Envelope in a Copy Number- and Lamin-Dependent Manner




B.D. Towbin, P. Meister, B.L. Pike, and S.M. Gasser
The Mechanism of Nucleocytoplasmic Transport through the Nuclear Pore Complex
J. Tetenbaum-Novatt and M.P. Rout
Nuclear Pore Complexes: Guardians of the Nuclear Genome
M. Capelson, C. Doucet, and M.W. Hetzer
Structure and Function of the Perinucleolar Compartment in Cancer Cells
A. Slusarczyk, R. Kamath, C. Wang, D. Anchel, C. Pollock, M.A. Lewandowska, T. Fitzpatrick, D.P. Bazett-Jones, and S. Huang
Summary: The Nucleus A Close-Knit Community of Dynamic Structures
S. Henikoff

Author Index

Subject Index