May 2009

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

PLOS Genetics: published May 22, 2009 | https://doi.org/10.1371/journal.pgen.1000493

Reconstructing the History of Yeast Genomes

David Sankoff

PLOS Genetics: published May 15, 2009 | https://doi.org/10.1371/journal.pgen.1000483

Research Articles

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

Ryan Kelley, Trey Ideker

PLOS Genetics: published May 29, 2009 | https://doi.org/10.1371/journal.pgen.1000488

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

PLOS Genetics: published May 29, 2009 | https://doi.org/10.1371/journal.pgen.1000496

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

PLOS Genetics: published May 29, 2009 | https://doi.org/10.1371/journal.pgen.1000497

Cdc7p-Dbf4p Regulates Mitotic Exit by Inhibiting Polo Kinase

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

PLOS Genetics: published May 29, 2009 | https://doi.org/10.1371/journal.pgen.1000498

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

PLOS Genetics: published May 29, 2009 | https://doi.org/10.1371/journal.pgen.1000499

Female Meiotic Sex Chromosome Inactivation in Chicken

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

PLOS Genetics: published May 22, 2009 | https://doi.org/10.1371/journal.pgen.1000466

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

Di Chen, Emma Lynn Thomas, Pankaj Kapahi

PLOS Genetics: published May 22, 2009 | https://doi.org/10.1371/journal.pgen.1000486

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

PLOS Genetics: published May 22, 2009 | https://doi.org/10.1371/journal.pgen.1000487

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

PLOS Genetics: published May 22, 2009 | https://doi.org/10.1371/journal.pgen.1000489

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

PLOS Genetics: published May 22, 2009 | https://doi.org/10.1371/journal.pgen.1000490

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

PLOS Genetics: published May 22, 2009 | https://doi.org/10.1371/journal.pgen.1000491

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

PLOS Genetics: published May 22, 2009 | https://doi.org/10.1371/journal.pgen.1000492

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

PLOS Genetics: published May 22, 2009 | https://doi.org/10.1371/journal.pgen.1000494

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

PLOS Genetics: published May 15, 2009 | https://doi.org/10.1371/journal.pgen.1000477

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

Bingshan Li, Suzanne M. Leal

PLOS Genetics: published May 15, 2009 | https://doi.org/10.1371/journal.pgen.1000481

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

PLOS Genetics: published May 15, 2009 | https://doi.org/10.1371/journal.pgen.1000482

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

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

PLOS Genetics: published May 15, 2009 | https://doi.org/10.1371/journal.pgen.1000484

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

PLOS Genetics: published May 15, 2009 | https://doi.org/10.1371/journal.pgen.1000485

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

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000462

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

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000467

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

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000468

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

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000469

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

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000470

Widespread Genomic Signatures of Natural Selection in Hominid Evolution

Graham McVicker, David Gordon, Colleen Davis, Phil Green

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000471

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

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000472

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

Raghuvar Dronamraju, James M. Mason

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000473

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

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000474

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

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000475

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

PLOS Genetics: published May 8, 2009 | https://doi.org/10.1371/journal.pgen.1000476

Cover

How does gene loss affect function in surviving paralogs?

Perspectives

Related Articles

Related Articles

Research Articles

Related Articles

Related Articles