title: Genome organization and reorganization in evolution: formatting for computation and function.
abstract: This volume deals with the role of epigenetics in life and evolution. The most dynamic forms of functional genome formatting involve DNA interacting with cellular complexes that do not alter sequence information. Such important epigenetic phenomena are the main subjects of other articles in this volume. This article focuses on the long-lived form of genome formatting that lies within the DNA sequence itself. I argue for a computational view of genome function as the long-term information storage organelle of each cell. Structural formatting consists of organizing various signals and coding sequences into computationally ready systems facilitating genome expression and genome transmission. The basic features of genome organization can be understood by examining the E. coli lac operon as a paradigmatic genomic system. Multiple systems are connected through distributed signals and repetitive DNA to form higher-order genome system architectures. Molecular discoveries about mechanisms of DNA restructuring show that cells possess the natural genetic engineering functions necessary for evolutionary change by rearranging genomic components and reorganizing system architectures. The concepts of cellular computation and decision-making, genome system architecture, and natural genetic engineering combine to provide a new way of framing evolutionary theories and understanding genome sequence information.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA. jsha@midway.uchicago.edu
authors.forename: James A
authors.initials: JA
authors.lastname: Shapiro
mesh_terms: D000818:Animals; D004269:DNA, Bacterial / Q000235:genetics; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D005818:Genetic Engineering; D016680:Genome, Bacterial; D006801:Humans; D008957:Models, Genetic; D008967:Molecular Biology
chemical_list: D004269:DNA, Bacterial