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Table of Contents | May 2009

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How does gene loss affect function in surviving paralogs?

Retinoic acid signaling controls vertebrate eye development; yet, different lineages of vertebrates have different numbers of genes that encode the Aldh enzyme that synthesizes retinoic acid. Mammals have three Aldh genes, zebrafish and stickleback (top and bottom) have two, and medaka (middle) has just one. Comparative genomic analyses reveal the history of Aldh gene duplication and loss (see Cañestro et al., 10.1371/journal.pgen.1000496) and suggest a mechanistic model for the acquisition or modification of subfunctions in surviving paralogs that preserve ancestral developmental programs in the face of gene loss, with implications for connectivities of human and model organism genomes.

Image Credit: Pictures taken by Dr. Cristian Cañestro in Dr. John H. Postlethwait's laboratory (Institute of Neuroscience, University of Oregon).

Perspectives

XY and ZW: Is Meiotic Sex Chromosome Inactivation the Rule in Evolution?

Satoshi H. Namekawa, Jeannie T. Lee

Reconstructing the History of Yeast Genomes

David Sankoff

Research Articles

Genome-Wide Fitness and Expression Profiling Implicate Mga2 in Adaptation to Hydrogen Peroxide

Ryan Kelley, Trey Ideker

Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes

Cristian Cañestro, Julian M. Catchen, Adriana Rodríguez-Marí, Hayato Yokoi, John H. Postlethwait

Iron-Sulfur (Fe/S) Protein Biogenesis: Phylogenomic and Genetic Studies of A-Type Carriers

Daniel Vinella, Céline Brochier-Armanet, Laurent Loiseau, Emmanuel Talla, Frédéric Barras

Cdc7p-Dbf4p Regulates Mitotic Exit by Inhibiting Polo Kinase

Charles T. Miller, Carrie Gabrielse, Ying-Chou Chen, Michael Weinreich

Sensory Ataxic Neuropathy in Golden Retriever Dogs Is Caused by a Deletion in the Mitochondrial tRNA^Tyr Gene

Izabella Baranowska, Karin Hultin Jäderlund, Inger Nennesmo, Erik Holmqvist, Nadja Heidrich, Nils-Göran Larsson, Göran Andersson, E. Gerhart H. Wagner, Åke Hedhammar, Rolf Wibom, Leif Andersson

Female Meiotic Sex Chromosome Inactivation in Chicken

Sam Schoenmakers, Evelyne Wassenaar, Jos W. Hoogerbrugge, Joop S. E. Laven, J. Anton Grootegoed, Willy M. Baarends

HIF-1 Modulates Dietary Restriction-Mediated Lifespan Extension via IRE-1 in Caenorhabditis elegans

Di Chen, Emma Lynn Thomas, Pankaj Kapahi

CA8 Mutations Cause a Novel Syndrome Characterized by Ataxia and Mild Mental Retardation with Predisposition to Quadrupedal Gait

Seval Türkmen, Gao Guo, Masoud Garshasbi, Katrin Hoffmann, Amjad J. Alshalah, Claudia Mischung, Andreas Kuss, Nicholas Humphrey, Stefan Mundlos, Peter N. Robinson

Adaptive Variation Regulates the Expression of the Human SGK1 Gene in Response to Stress

Francesca Luca, Sonal Kashyap, Catherine Southard, Min Zou, David Witonsky, Anna Di Rienzo, Suzanne D. Conzen

Admixture Mapping of 15,280 African Americans Identifies Obesity Susceptibility Loci on Chromosomes 5 and X

Ching-Yu Cheng, W. H. Linda Kao, Nick Patterson, Arti Tandon, Christopher A. Haiman, Tamara B. Harris, Chao Xing, Esther M. John, Christine B. Ambrosone, Frederick L. Brancati, Josef Coresh, Michael F. Press, Rulan S. Parekh, Michael J. Klag, Lucy A. Meoni, Wen-Chi Hsueh, Laura Fejerman, Ludmila Pawlikowska, Matthew L. Freedman, Lina H. Jandorf, Elisa V. Bandera, Gregory L. Ciupak, Michael A. Nalls, Ermeg L. Akylbekova, Eric S. Orwoll, Tennille S. Leak, Iva Miljkovic, Rongling Li, Giske Ursin, Leslie Bernstein, Kristin Ardlie, Herman A. Taylor, Eric Boerwinckle, Joseph M. Zmuda, Brian E. Henderson, James G. Wilson, David Reich

Murine Leukemias with Retroviral Insertions at Lmo2 Are Predictive of the Leukemias Induced in SCID-X1 Patients Following Retroviral Gene Therapy

Utpal P. Davé, Keiko Akagi, Rati Tripathi, Susan M. Cleveland, Mary A. Thompson, Ming Yi, Robert Stephens, James R. Downing, Nancy A. Jenkins, Neal G. Copeland

Root Suberin Forms an Extracellular Barrier That Affects Water Relations and Mineral Nutrition in Arabidopsis

Ivan Baxter, Prashant S. Hosmani, Ana Rus, Brett Lahner, Justin O. Borevitz, Balasubramaniam Muthukumar, Michael V. Mickelbart, Lukas Schreiber, Rochus B. Franke, David E. Salt

GLS-1, a Novel P Granule Component, Modulates a Network of Conserved RNA Regulators to Influence Germ Cell Fate Decisions

Agata Rybarska, Martin Harterink, Britta Jedamzik, Adam P. Kupinski, Mark Schmid, Christian R. Eckmann

Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip

Chris C. A. Spencer, Zhan Su, Peter Donnelly, Jonathan Marchini

Discovery of Rare Variants via Sequencing: Implications for the Design of Complex Trait Association Studies

Bingshan Li, Suzanne M. Leal

MSH2 ATPase Domain Mutation Affects CTG•CAG Repeat Instability in Transgenic Mice

Stéphanie Tomé, Ian Holt, Winfried Edelmann, Glenn E. Morris, Arnold Munnich, Christopher E. Pearson, Geneviève Gourdon

Multipotent Genetic Suppression of Retrotransposon-Induced Mutations by Nxf1 through Fine-Tuning of Alternative Splicing

Dorothy Concepcion, Lisbeth Flores-García, Bruce A. Hamilton

Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

Jonathan L. Gordon, Kevin P. Byrne, Kenneth H. Wolfe

Probing the Functional Impact of Sequence Variation on p53-DNA Interactions Using a Novel Microsphere Assay for Protein-DNA Binding with Human Cell Extracts

Maher A. Noureddine, Daniel Menendez, Michelle R. Campbell, Omari J. Bandele, Monica M. Horvath, Xuting Wang, Gary S. Pittman, Brian N. Chorley, Michael A. Resnick, Douglas A. Bell

Tor1/Sch9-Regulated Carbon Source Substitution Is as Effective as Calorie Restriction in Life Span Extension

Min Wei, Paola Fabrizio, Federica Madia, Jia Hu, Huanying Ge, Lei M. Li, Valter D. Longo

Evaluation of Haplotype Inference Using Definitive Haplotype Data Obtained from Complete Hydatidiform Moles, and Its Significance for the Analyses of Positively Selected Regions

Koichiro Higasa, Yoji Kukita, Kiyoko Kato, Norio Wake, Tomoko Tahira, Kenshi Hayashi

Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution

John K. Pace II, Shurjo K. Sen, Mark A. Batzer, Cédric Feschotte

SWI/SNF Associates with Nascent Pre-mRNPs and Regulates Alternative Pre-mRNA Processing

Anu Tyagi, Jessica Ryme, David Brodin, Ann Kristin Östlund Farrants, Neus Visa

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

Graham McVicker, David Gordon, Colleen Davis, Phil Green

Linkage Disequilibrium between Two High-Frequency Deletion Polymorphisms: Implications for Association Studies Involving the glutathione-S transferase (GST) Genes

Yongzhong Zhao, Michael Marotta, Evan E. Eichler, Charis Eng, Hisashi Tanaka

Recognition of Double Strand Breaks by a Mutator Protein (MU2) in Drosophila melanogaster

Raghuvar Dronamraju, James M. Mason

Ancient mtDNA Genetic Variants Modulate mtDNA Transcription and Replication

Sarit Suissa, Zhibo Wang, Jason Poole, Sharine Wittkopp, Jeanette Feder, Timothy E. Shutt, Douglas C. Wallace, Gerald S. Shadel, Dan Mishmar

The Yeast Pif1 Helicase Prevents Genomic Instability Caused by G-Quadruplex-Forming CEB1 Sequences In Vivo

Cyril Ribeyre, Judith Lopes, Jean-Baptiste Boulé, Aurèle Piazza, Aurore Guédin, Virginia A. Zakian, Jean-Louis Mergny, Alain Nicolas

Microdissection of Shoot Meristem Functional Domains

Lionel Brooks III, Josh Strable, Xiaolan Zhang, Kazuhiro Ohtsu, Ruilian Zhou, Ananda Sarkar, Sarah Hargreaves, Robert J. Elshire, Douglas Eudy, Teresa Pawlowska, Doreen Ware, Diane Janick-Buckner, Brent Buckner, Marja C. P. Timmermans, Patrick S. Schnable, Dan Nettleton, Michael J. Scanlon

Yeast Silent Mating Type Loci Form Heterochromatic Clusters through Silencer Protein-Dependent Long-Range Interactions

Adriana Miele, Kerstin Bystricky, Job Dekker

Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference

Eric A. Stone, Julien F. Ayroles

synaptojanin1 Is Required for Temporal Fidelity of Synaptic Transmission in Hair Cells

Josef G. Trapani, Nikolaus Obholzer, Weike Mo, Susan E. Brockerhoff, Teresa Nicolson

Large-Scale Selective Sweep among Segregation Distorter Chromosomes in African Populations of Drosophila melanogaster

Daven C. Presgraves, Pierre R. Gérard, Anjuli Cherukuri, Terrence W. Lyttle

Epistatic Module Detection for Case-Control Studies: A Bayesian Model with a Gibbs Sampling Strategy

Wanwan Tang, Xuebing Wu, Rui Jiang, Yanda Li

Buffering of Segmental and Chromosomal Aneuploidies in Drosophila melanogaster

Per Stenberg, Lina E. Lundberg, Anna-Mia Johansson, Patrik Rydén, Malin J. Svensson, Jan Larsson

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