The Implicit Genome

by Lynn Helena Caporale

Overview

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.

Product Details

ISBN-13:	9780195172713
Publisher:	Oxford University Press
Publication date:	02/02/2006
Pages:	400
Product dimensions:	9.20(w) x 6.10(h) x 0.80(d)

About the Author

Dr. Lynn Helena Caporale received her Ph.D. in Molecular Biology from the University of California at Berkeley and is the author of Darwin and the Genome. She is the Associate Director for Comparative Genomics at the Judith P. Sulzberger Genome Center at Columbia University.

Table of Contents

An Overview of the Implicit Genome, Lynn Helena Caporale1. Sequence-Dependent Properties of DNA and Their Role in Function, Donald M. Crothers2. Mutation as a Phenotype, Errol C. Friedberg3. Repeats and Variation in Pathogen Selection, Christopher D. Bayliss and E. Richard Moxon4. 4. Tuning Knobs in the Genome: Evolution of Simple Sequence Repeats by Indirect Selection, David G. King, Edward N. Trifonov, Yechezkel Kashi5. Implicit Information in Eukaryotic Pathogens as the Basis of Antigenic Variation, J. Dave Barry6. The Role of Repeat Sequences in Bacterial Genetic Adaptation to Stress, Eduardo P. C. Rocha7. The Role of Mobile DNA in the Evolution of Prokaryotic Genomes, Gary Myers, Ian Paulsen, and Claire Fraser8. Eukaryotic Transposable Elements: Teaching Old Genomes New Tricks, Susan R. Wessler9. Immunoglobulin Recombination Signal Sequences: Somatic and Evolutionary Functions, Ellen Hsu10. Somatic Evolution and Antibody Genes, Rupert Beale and Dagmer Iber11. Regulated and Unregulated Recombination of G-rich Genomic Regions, Nancy Maizels12. The Role of the Genome in the Initiation of Meiotic Recombination, Rhona H. Borts and David T. Kirkpatrick13. Nuclear Duality and the Genesis of Unusual Genomes in Ciliated Protozoa, Carolyn L. Jahn14. Editing Informational Content of Expressed DNA Sequences and Their Transcripts, Harold C. Smith15. Alternative Splicing: One Gene, Many Products, Brenton R. Graveley16. Imprinting: the Hidden Genome, Alyson Ashe and Emma WhitelawEpilogue: An Engineering Perspective: The Implicit Protocols, John Doyle, Marie Csete, and Lynn CaporaleReferences

Editorial Reviews

"Maintains an excitement that typically is only found in texts for a lay audience"—Elizabeth A.D. Hammock, Postdoctoral Research Fellow, Vanderbilt University

"The Implicit Genome explains why the greatest challenge of today's genomics is to annotate the biological functions of DNA sequences. The language of genomes is written in a simple alphabet of As, Ts, Gs, and Cs, but it is so rich in idiom that biological function is difficult to infer from sequence alone. Even regions that code for proteins are problematical because of imprinting, alternative splicing, RNA editing, and other complexities. Lynn Caporale has done a great service in highlighting some of the major challenges in contemporary genomics."—Dan Hartl, Higgins Professor of Biology, Harvard University, and Member National Academy of Sciences

"This timely, critical evaluation of...undeciphered genomic information is of interest both for life scientists and for all those who are fascinated by the natural driving forces of life and its evolution."—Werner Arber, Emeritus Professor of Molecular Microbiology, University of Basel, Switzerland, and Nobel Laureate in Medicine

"The book, through paradigmatic experiments and analysis...points to avenues of research that could lead to a much more thorough understanding of the combinatorial wealth of surprises the genome still holds for us."—Dennis Shasha, Professor, Courant Institute of Mathematical Sciences, New York University, and editor of the Oxford Series in Systems Biology

From the Publisher