Over the past half-century, the central dogma, in which DNA makes RNA makes protein, has dominated thinking in biology, with continuing refinements in understanding of DNA inheritance, gene expression, and macromolecular interactions. However, we have also witnessed the elucidation of epigenetic phenomena that violate conventional notions of inheritance. Protein-only inheritance involves the transmission of phenotypes by self-perpetuating changes in protein conformation. Proteins that constitute chromatin can also transmit heritable information, for example, via posttranslational modifications of histones. Both the transmission of phenotypes via the formation of protein conformations and the inheritance of chromatin states involve self-perpetuating assemblies of proteins, and there is evidence for some common structural features and conceptual frameworks between them. To foster interactions between researchers in these two fields, the National Academy of Sciences convened an Arthur M.Sackler Colloquium entitled “Self-Perpetuating Structural States in Biology, Disease, and Genetics” in Washington, DC, on March 22–24, 2002. Participants described new phenomenology and provided insights into fundamental mechanisms of protein and chromatin inheritance. Perhaps most surprising to attendees was emerging evidence that these unconventional modes of inheritance may be common.

Contents

• Arthur M. Sackler, M.D.
• Self-perpetuating structural states in biology, disease, and genetics
• Transmission of prions
  • “Natural” Transmission of Prions
  • Iatrogenic Transmission of Prions
  • Experimental Transmission of Surface-Bound Prions
  • Concluding Remarks
• Conservation of a portion of the S. cerevisiae Ure2p prion domain that interacts with the full-length protein
  • Materials and Methods
  • Results
  • Discussion
• Interactions among prions and prion “strains” in yeast
  • Materials and Methods
  • Results
  • Discussion
• Identification of benzothiazoles as potential polyglutamine aggregation inhibitors of Huntington's disease by using an automated filter retardation assay
  • Materials and Methods
  • Results
  • Discussion
• Chaperoning brain degeneration
  • Materials and Methods
  • A Drosophila Model for Human Neurodegenerative Disease
  • The Molecular Chaperone Hsp70 Is a Potent Suppressor of Polyglutamine Pathogenicity
  • Chaperone Suppression of α-Synuclein Toxicity in a Drosophila Model for Parkinson's Disease
  • Endogenous Chaperone Activity Plays a Role in α-Synuclein Toxicity in Drosophila and Potentially also in Parkinson's Disease
  • Discussion
• Molecular chaperones as modulators of polyglutamine protein aggregation and toxicity
  • Mechanism of polyQ Aggregation
  • Relationship Between polyQ Aggregation and Toxicity
  • Transcriptional Dysregulation by polyQ Aggregation
  • Role of Molecular Chaperones in polyQ Aggregation and Toxicity
  • Role of the Ubiquitin-Proteasome System in polyQ Aggregation and Toxicity
  • Perspectives
• Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases
  • Materials and Methods
  • Results
  • Discussion
  • Conclusion
• Sequence-dependent denaturation energetics: A major determinant in amyloid disease diversity
  • Methods
  • Results and Discussion
• The insulation of genes from external enhancers and silencing chromatin
  • An Insulator as an Enhancer-Blocking Element
  • Insulators as Barriers
  • Conclusion
• Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast
  • Materials and Methods
  • Results
  • Discussion
• Changes in the middle region of Sup35 profoundly alter the nature of epigenetic inheritance for the yeast prion [PSI+]
  • Materials and Methods
  • Results
  • Discussion
• Heritable chromatin structure: Mapping “memory” in histones H3 and H4
  • Materials and Methods
  • Results
  • Discussion
• Does heterochromatin protein 1 always follow code?
  • HP1 Follows Code
  • Are There Multiple Mechanisms for HP1 Association?
  • HP1 Interacts with a Myriad of Proteins
  • HP1 Regulates Gene Expression
• Self-perpetuating epigenetic pili switches in bacteria
  • Cis- and Trans-Acting Pap Switch Components
  • Pap Phase Variation Model
  • Switch Inputs
  • Outputs
• Histone H3 variants specify modes of chromatin assembly
  • H3 Variants Determine the Nucleosome Assembly Pathway
  • Centromeres Replicate Before Their Surrounding Heterochromatin
  • High-Resolution Mapping of Centromere Replicons
  • Inferring the RI Machinery
  • Opening a Space for Histone Replacement
  • The RI Target Sites for H3 Variants Are in Distinct Nuclear Compartments
  • Why RI Assembly?
  • Conclusions
• Induction and maintenance of nonsymmetrical DNA methylation in Neurospora
  • Maintenance Methylation in Neurospora
  • Clues to Involvement of Methyl/RIP-DNA Binding Proteins and Histone Deacetylation in DNA Methylation
  • The DIM-5 Histone Methyltransferase Integrates Histone Code Information and Controls DNA Methylation
• Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes
  • Materials and Methods
  • Results
  • Discussion
• RNA-directed DNA methylation in Arabidopsis
  • Experimental Procedures
  • Results
  • Discussion
• Program
• National Academy of Sciences Sackler Colloquia Series

This work is reprinted from the Proceedings of the National Academy of Sciences of the United States of America, vol. 99, suppl. 4, pp. 16377–16506, December 10, 2002, and includes articles from the Arthur M.Sackler Colloquium on Self-Perpetuating Structural States in Biology, Disease, and Genetics, held at the National Academy of Sciences in Washington, DC, March 22–24, 2002. The articles appearing in these pages were contributed by speakers at the colloquium and were anonymously reviewed, but they have not been independently reviewed by the Academy. Any opinions, findings, conclusions, or recommendations expressed in this work are those of the authors and do not necessarily reflect the views of the National Academy of Sciences.

The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the U.S. Congress in 1863, the Academy has a mandate that requires it to advise the Federal Government on scientific and technical matters.