˜Theœ implicit genome

For over half a century, we have been in the thrall of the double-helicaln structure of DNA, which, in an instant, revealed that information can be transferred between generations by a simple rule, A pairs with T, G pairs with C. In its beautiful simplicity, this structure, along with the table of codons worked out in the following decade, had entranced us into believing that we can fully understand the information content of a DNA sequence, simply by treating it as text that is read in a linear fashion. While we have learned much based on this assumption, there is much we have missed. Far from a passive tape running through a reader, genomes contain information that appears in new forms which create regions with distinct behavior. Some are gene rich, some mobile, some full of repeats and duplications, some sticking together across long evolutionary distances, some readily breaking apart in tumor cells. Even protein-coding regions can carry additional information, taking advantage of the flexible coding options provided by the degeneracy of the genetic code. The chapters in this volume touch on one or more of three interconnected themes; information can be implied, rather than explicit, in a genome; information can lead to focused and/or regulated changes in nucleotide sequences; information that affects the probability of distinct classes of mutation has implications for evolutionary theory. Contents......Page 9 Contributors......Page 11 An Overview of the Implicit Genome......Page 17 1. Sequence-Dependent Properties of DNA and Their Role in Function......Page 37 2. Mutation as a Phenotype......Page 53 3. Repeats and Variation in Pathogen Selection......Page 68 4. Tuning Knobs in the Genome: Evolution of Simple Sequence Repeats by Indirect Selection......Page 91 5. Implicit Information in Eukaryotic Pathogens as the Basis of Antigenic Variation......Page 105 6. The Role of Repeat Sequences in Bacterial Genetic Adaptation to Stress......Page 121 7. The Role of Mobile DNA in the Evolution of Prokaryotic Genomes......Page 135 8. Eukaryotic Transposable Elements: Teaching Old Genomes New Tricks......Page 152 9. Immunoglobulin Recombination Signal Sequences: Somatic and Evolutionary Functions......Page 177 10. Somatic Evolution of Antibody Genes......Page 191 11. Regulated and Unregulated Recombination of G-rich Genomic Regions......Page 205 12. The Role of the Genome in the Initiation of Meiotic Recombination......Page 222 13. Nuclear Duality and the Genesis of Unusual Genomes in Ciliated Protozoa......Page 239 14. Editing Informational Content of Expressed DNA Sequences and Their Transcripts......Page 262 15. Alternative Splicing: One Gene, Many Products......Page 280 16. Imprinting: The Hidden Genome......Page 296 Epilogue: An Engineering Perspective: The Implicit Protocols......Page 308 References......Page 313 List of Acronyms......Page 377 A......Page 379 B......Page 380 C......Page 381 D......Page 383 E......Page 385 F......Page 386 G......Page 387 H......Page 388 I......Page 389 M......Page 390 O......Page 392 P......Page 393 R......Page 394 S......Page 395 T......Page 397 W......Page 398 Z......Page 399 Sequence-dependent Properties Of Dna And Their Role In Function / Donald Crothers -- Mutation As A Phenotype / Errol C. Friedberg -- Repeats And Variation In Pathogen Selection / Chris Bayliss And Richard Moxon -- Tuning Knobs In The Genome: Evolution Of Simple Sequence Repeats By Indirect Selection / David G. King, Edward N. Trifonov, Yechezkel Kashi -- Implicit Information In Eukaryotic Pathogens As The Basis Of Antigenic Variation / J. Dave Barry -- The Role Of Repeat Sequences In Bacterial Genetic Adaptation To Stress / Eduardo P.c. Rocha -- The Role Of Mobile Dna In The Evolution Of Prokaryotic Genomes / Ian Paulsen & Claire Fraser -- Eukaryotic Transposable Elements: Teaching Old Genomes New Tricks / Susan R. Wessler -- Assembling Genes In The Immune System / Ellen Hsu -- Focused Mutation In The Immune System / Rupert Beale, Dagmar Iber -- Regulated And Unregulated Recombination Of G-rich Genomic Regions / Nancy Maizels -- The Role Of The Genome In The Initiation Of Meiotic Recombination / Rhona H. Borts & David T. Kirkpatrick -- Nuclear Duality And The Genesis Of Unusual Genomes In Ciliated Protozoa / Carolyn Jahn -- Editing Informational Content Of Expressed Dna Sequences And Their Transcripts / Harold C. Smith -- Alternative Splicing / Brenton Graveley -- Imprinting; The Hidden Genome / Alyson Ashe And Emma Whitelaw. Edited By Lynn Helena Caporale. Includes Bibliographical References And Index. "Most analyses assume that genomes are to be read as linear text, much as a sequence of nucleotides can be translated into a sequence of amino acids by looking in a table. However, information can evolve in genomes with distinct forms of representation, such as in the structure of DNA or RNA and/or the relationship between nucleotide sequences. Such information has importance to biology yet is largely unexpected and unexplored. As described in this volume, much of this information, through mechanisms ranging from alternative splicing of RNA to the generation of bacterial coat protein diversity, affects the probability of distinct types of alterations in the nucleic acid sequence. Some genomic DNA sequences affect genome stability, handling and organization, with implications for the robustness of lineages over evolutionary time. The examples reviewed in this volume, taken from a broad range of biological organisms, both extend our view of the nature of information encoded within genomes, and can deepen our appreciation of the power of natural selection, through which this information, in its various forms, has emerged." -- Publisher Discusses three interconnected themes: information can be implied, rather than explicit, in a genome; information can lead to focused and/or regulated changes in nucleotide sequences; and information that affects the probability of distinct classes of mutation has implications for evolutionary theory