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1 Sex and the Single Chromosome Victoria H. Meller and Mitzi I. Kuroda The Evolution of Sex Chromosomes Selective Pressure Has Led to a Variety of Dosage-Compensation Mechanisms Dosage Compensation in Drosophila by the MSL Complex A Series of Binary Switches Regulates the Sex Specificity of Dosage Compensation in Drosophila Sex lethal Communicates the X:A Ratio to the Dosage-Compensation Pathway through Repression of msl2 Translation Evidence for the Coexistence of a Female-Specific Dosage-Compensation Pathway in Drosophila MSL-Mediated Dosage Compensation Spreads from Special Entry Sites in cis The Behavior of MSL Complexes on Paired Chromosomes Noncoding RNAs, Epigenetic Regulation, and Chromatin Structure References 2 Is X-Chromosome Inactivation a Homology Effect? Jeannie T. Lee The Phenomenon of X Inactivation Control Elements Current Models of Xist Regulation Evidence for Additional Control Elements in Random X Inactivation Is X Inactivation a Homology Effect? Conclusions References 3 Homologous Chromosome Associations and Nuclear Order in Meiotic and Mitotically Dividing Cells of Budding Yeast Sean M. Burgess Introduction The Global Arrangement of Chromosomes in the Nucleus Homology Recognition during DNA Double-Strand Break Repair Pairing and Synapsis of Homologous Chromosomes during Meiosis Homolog Interactions in Mitotically Dividing Cells (Vegetative Pairing) Concluding Remarks References 4 The Role of Sequence Homology in the Repair of DNA Double-Strand Breaks in Drosophila Gregory B. Gloor Introduction The Effect of Sequence Identity on Gene Conversion The Effect of the Extent of Donor Homology on Double-Strand Break Repair The Effect of the Extent of Recipient Homology on Double-Strand Break Repair 101 The Effect of Donor Location on Double-Strand Break Repair The Effect of Chromosome Pairing on Double-Strand Break Repair Summary References 5 The Origins of Genomic Imprinting in Mammals Frank Sleutels and Denise P. Barlow Introduction Definition of Genomic Imprinting Evolution and Function of Imprinting Origins of Genomic Imprinting Predictions for an Imprinting Mechanism Organization and Epigenetic Modification of Imprinted Genes DNA Methylation and Genomic Imprints The Function of Methylation Imprints: Model C Innocent Bystanders, Future Challenges Concluding Remarks References 6 Genomic Imprinting during Seed Development Celia Baroux, Charles Spillane, and Ueli Grossniklaus Introduction Historical Overview Genome-Wide Imprinting Gene-Specific Imprinting and the Control of Seed Development Conclusion References 7 Long-Distance Cis and Trans Interactions Mediate Paramutation Vicki L. Chandler, Maike Stam, and Lyudmila V. Sidorenko Introduction Background and Definitions Paramutation at bl and pl Models for Paramutation Implications and Possible Functions References 8 Homology-Dependent Gene Silencing and Host Defense in Plants Marjori A. Matzke, Werner Aufsatz, Tatsuo Kanno, M. Florian Mette, andAntonius J. M. Matzke Introduction RNA Silencing; DNA-DNA Pairing Homology-Dependent Gene Silencing (HDGS) in Genomic Imprinting and X-Chromosome Inactivation in Mammals HDGS and the Host Genome Defense: Evolutionary Aspects Summary and Conclusions References 9 Quelling in Neurospora crassa Annette S. Pickford, Caterina Catalanotto, Carlo Cogoni, and Giuseppe Macino Introduction The Discovery of Quelling in Neurospora The Quest for quelling-defective (qde) Mutants Isolation of the Genes Involved in Quelling in Neurospora A Unified Model for Quelling, Co-suppression, and RNA Interference Supporting Evidence for the Proposed Model The Search for Additional PTGS Components Conclusions References 10 Non-Mendelian Inheritance and Homology-Dependent Effects in Ciliates Eric Meyer and Olivier Garnier Introduction Regulation of IES Excision by Homology-Dependent Maternal Effects Regulation of Zygotic Genome Amplification and Chromosome Fragmentation by Homology-Dependent Maternal Effects Conclusions References 11 RNAi (Nematodes: Caenorhabditis elegans) Alla Grishok and Craig Mello Introduction/History RNAi and Other Silencing Mechanisms in C. elegans Spreading and Persistence of RNAi Molecular Mechanism of RNAi Components of the RNAi Pathway RNAi and Development References 12 Antisense RNAs in Bacteria and Their Genetic Elements E. Gerhart H. Wagner, Shoshy Altuvia, and Pascale Romby Introduction-Antisense Principle and Gene Regulation Naturally Occurring Antisense RNA Control Systems Antisense RNA Mechanisms and Biological Context Antisense Structure and Kinetics of Binding Matching Antisense RNA Properties with Biological Roles Concluding Remarks References 13 Transvection in Drosophila James A. Kennison and Jeffrey W. Southworth Introduction Historical Background to Bithorax-Complex Transvection Transvection, trans Sensing, and Homology Effects Trans-Acting zeste Proteins and Transvection "Critical Regions" for Transvection References 14 Pairing-Sensitive Silencing, Polycomb Group Response Elements, and Transposon Homing in Drosophila Judith A. Kassis Introduction Three Types of mini-white Silencing mini-white Silencing by PREs - Effect of Mutations in Polycomb Group Genes on mini-white Silencing mini-white Silencing by Other Elements Is the engrailed PS Fragment a PRE? Pleiohomeotic, PREs and PS Sites Not All PS Sites Are PREs and Vice Versa Pairing-Sensitive Silencing Has Not Been Demonstrated in the Embryo Transposon Homing Preferential Insertion of PRE-Containing Transposons Near Endogenous PREs Conclusions References 15 Repeat-induced Gene Silencing in Fungi Eric U. Selker Introduction Discovery and Basic Features of RIP and MIP De Novo and Maintenance Methylation Associated with MIP and RIP Consequences of RIP and MIP Concluding Remarks References 16 The Evolution of Gene Duplicates Sarah P. Otto and Paul Yong Introduction Evolutionary Forces Affecting Gene Copy Number Discussion Appendix: Modeling the Invasion of a Duplicate Gene References 17 Prions of Yeast as Epigenetic Phenomena: High Protein "Copy Number" Inducing Protein "Silencing" Reed B. Wickner, Herman K. Edskes, B. Tibor Roberts, Michael Pierce, and Ulrich Baxa Introduction Three Genetic Criteria for Prions [URE3] as a Prion of the Ure2 Protein Self-Propagating Ure2p Amyloid Is the [URE3] Prion MKS1 Is Necessary tor de Novo Generation of the [URE3] Prion Chaperones Affecting [URE3] Propagation [PSI] as a Prion of the SUP35 Protein Chaperones and [PSI+] Portable Prion Domains and Synthetic Prions Curing of [URE3] and [PSI+] [Het-s], a Prion with a Normal Cellular Function Are Yeast Prions Adaptive, a Cellular Stress, or Both? [PIN+] Is Required for Inducibility of [PSI+] [KIL-d] Is an Epigenetic Phenomenon: Is It a Prion? Are Transmissible Spongiform Encephalopathies of Mammals Due to Prions? Conclusions References Index