Nuclear Organization & Function

Symposium Participants v Foreword xix 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 1 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 11 Cell Signaling and Transcriptional Regulation via Histone Phosphorylation S.L. Berger 23 HIRA and Daxx Constitute Two Independent Histone H3.3-Containing Predeposition Complexes S.J. Elsaesser and C.D. Allis 27 The INO80 Family of Chromatin-Remodeling Enzymes: Regulators of Histone Variant Dynamics S. Watanabe and C.L. Peterson 35 Role of K3K27 Demethylases Jmjd3 and UTX in Transcriptional Regulation M.R. Hüand D.L. Spector 43 Epigenetic Inheritance of Centromeres S. Henikoff and T. Furuyama 51 Functional Dissection of Polycomb Repressive Complex 1 Reveals the Importance of a Charged Domain D.J. Grau, J.M. Antao, and R.E. Kingston 61 Histone Acetylation and the Maintenance of Chromatin Compaction by Polycomb Repressive Complexes R. Eskeland, E. Freyer, M. Leeb, A. Wutz, and W.A. Bickmore 71 Chromatin Boundaries, Insulators, and Long-Range Interactions in the Nucleus K.E. Giles, H. Gowher, R. Ghirlando, C. Jin, and G. Felsenfeld 79 Transcription and Beyond Nuclear Origins of Cell-to-Cell Variability Z. Waks and P.A. Silver 87 The Role of Cotranscriptional Histone Methylations S. Buratowski and T. Kim 95 Chromatin and Alternative Splicing M. Alló.E. Schor, M.J. Muñ M. de la Mata, E. Agirre, J. Valcáel, E. Eyras, and A.R. Kornblihtt 103 Nuclear Physics: Quantitative Single-Cell Approaches to Nuclear Organization and Gene Expression T. Lionnet, B. Wu, D. Grü, R.H. Singer, and D.R. Larson 113 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 127 DNA Replication and Genome Integrity The Many Faces of Redundancy in DNA Replication Control J.F.X. Diffley 135 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 143 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 155 How Shelterin Solves the Telomere End-Protection Problem T. de Lange 167 The Smc5/6 Complex: More than Repair? A. Kegel and C. Sjön 179 Reprogramming and Differentiation Efficiencies and Mechanisms of Nuclear Reprogramming V. Pasque, K. Miyamoto, and J.B. Gurdon 189 Gene Targeting in Human Pluripotent Cells D. Hockemeyer and R. Jaenisch 201 Epigenetic Reprogramming of Mouse Germ Cells toward Totipotency M.A. Surani and P. Hajkova 211 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 219 Connecting Transcriptional Control to Chromosome Structure and Human Disease J.J. Newman and R.A. Young 227 Transcription Factors for the Modulation of Pluripotency and Reprogramming J.-C.D. Heng, Y.L. Orlov, and H.-H. Ng 237 Changes in Chromatin Fiber Density as a Marker for Pluripotency E. Fussner, K. Ahmed, H. Dehghani, M. Strauss, and D.P. Bazett-Jones 245 Cancer Epigenetics: From Disruption of Differentiation Programs to the Emergence of Cancer Stem Cells P. Scaffidi and T. Misteli 251 Heterochromatin Formation and Gene Silencing Assembly and Functions of Heterochromatin in the Fission Yeast Genome O. Aygü S.I.S. Grewal 259 Germline Reprogramming of Heterochromatin in Plants K.M. Creasey and R.A. Martienssen 269 On the Connection between RNAi and Heterochromatin at Centromeres E. Lejeune, E.H. Bayne, and R.C. Allshire 275 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 285 Transcriptional Interference and Gene Orientation in Yeast: Noncoding RNA Connections M. Gullerova and N.J. Proudfoot 299 Nuclear Bodies and RNA Biology Cajal Bodies and Histone Locus Bodies in Drosophila and Xenopus Z.F. Nizami, S. Deryusheva, and J.G. Gall 313 Down-Regulation of a Host microRNA by a Viral Noncoding RNA D. Cazalla and J.A. Steitz 321 Long Noncoding RNAs as Enhancers of Gene Expression U.A. Øom, T. Derrien, R. Guigo, and R. Shiekhattar 325 Chromatin Structure and Nuclear Organization Dynamics during X-Chromosome Inactivation E.P. Nora and E. Heard 333 XIST RNA and Architecture of the Inactive X Chromosome: Implications for the Repeat Genome L.L. Hall and J.B. Lawrence 345 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 357 Genetic Analysis of Nuclear Bodies: From Nondeterministic Chaos to Deterministic Order T.K. Rajendra, K. Praveen, and A.G. Matera 365 Chromosome Structure and Mitosis Splitting the Nucleus: What’s Wrong with the Tripartite Ring Model? K. Nasmyth and R.A. Oliveira 375 Physical Linkages between Sister Chromatids and Their Removal during Yeast Chromosome Segregation J. Baxter and L. Aragó89 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 395 Centromere Identity, Function, and Epigenetic Propagation across Cell Divisions B.E. Black, L.E.T. Jansen, D.R. Foltz, and D.W. Cleveland 403 Temporal and Spatial Regulation of Targeting Aurora B to the Inner Centromere Y. Watanabe 419 The Life Cycle of Centrioles E. Hatch and T. Stearns 425 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 433 New Insight into the Mitotic Chromosome Structure: Irregular Folding of Nucleosome Fibers Without 30-nm Chromatin Structure K. Maeshima, S. Hihara, and H. Takata 439 Thoughts on Aneuploidy E.M. Torres, B.R. Williams, Y.-C. Tang, and A. Amon 445 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 453 Chromatin Folding: From Linear Chromosomes to the 4D Nucleus T. Cheutin, F. Bantignies, B. Leblanc, and G. Cavalli 461 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 475 Window into the Complexities of Chromosome Interactomes A. Gör, A. Fernandez Woodbridge, C. Shi, E. Aurell, M. Imreh, and R. Ohlsson 493 Transcription Factories and Nuclear Organization of the Genome C.H. Eskiw, N.F. Cope, I. Clay, S. Schoenfelder, T. Nagano, and P. Fraser 501 Role of Nuclear Architecture in Epigenetic Alterations in Cancer H.P. Easwaran and S.B. Baylin 507 Nuclear Periphery Role of the Nuclear Lamina in Genome Organization and Gene Expression D. Peric-Hupkes and B. van Steensel 517 Nuclear Lamins in Cell Regulation and Disease T. Shimi, V. Butin-Israeli, S.A. Adam, and R.D. Goldman 525 Lamina-Independent Lamins in the Nuclear Interior Serve Important Functions T. Dechat, K. Gesson, and R. Foisner 533 Three-Dimensional Organization of Chromatids by Nuclear Envelope–Associated Structures G. Blobel 545 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 555 The Mechanism of Nucleocytoplasmic Transport through the Nuclear Pore Complex J. Tetenbaum-Novatt and M.P. Rout 567 Nuclear Pore Complexes: Guardians of the Nuclear Genome M. Capelson, C. Doucet, and M.W. Hetzer 585 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 599 Summary: The Nucleus - A Close-Knit Community of Dynamic Structures S. Henikoff 607 Author Index 617 Subject Index 619