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Table of Contents

December 2009

Cover

A colony of the pathogenic yeast Candida albicans grown on CHROMagar medium exhibits complex colony morphology.
Issue Image

In this issue of PLoS Genetics, Homann et al. report a phenotypic profile of the transcriptional network of Candida albicans. A library of transcription factor deletion strains was created and tested for growth and colony morphology phenotypes on over 50 different growth media. The resulting phenotypic profiles provide insight into the cellular role of many previously uncharacterized transcription factors and also provide new insight into the scope of the regulatory network governing the creation of complex colony morphologies in C. albicans.

Image Credit: Oliver Homann and Jeanselle Dea

Interview

The Eureka Moment: An Interview with Sir Alec Jeffreys

Jane Gitschier

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000765

Perspective

Retrotransposon Silencing by piRNAs: Ping-Pong Players Mark Their Sub-Cellular Boundaries

Shinichiro Chuma, Ramesh S. Pillai

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000770

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Research Articles

Increased Expression and Protein Divergence in Duplicate Genes Is Associated with Morphological Diversification

Kousuke Hanada, Takashi Kuromori, Fumiyoshi Myouga, Tetsuro Toyoda, Kazuo Shinozaki

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000781

Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes

Gregory Hannum, Rohith Srivas, Aude Guénolé, Haico van Attikum, Nevan J. Krogan, Richard M. Karp, Trey Ideker

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000782

A Phenotypic Profile of the Candida albicans Regulatory Network

Oliver R. Homann, Jeanselle Dea, Suzanne M. Noble, Alexander D. Johnson

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000783

Progressive Purkinje Cell Degeneration in tambaleante Mutant Mice Is a Consequence of a Missense Mutation in HERC1 E3 Ubiquitin Ligase

Tomoji Mashimo, Ouadah Hadjebi, Fabiola Amair-Pinedo, Toshiko Tsurumi, Francina Langa, Tadao Serikawa, Constantino Sotelo, Jean-Louis Guénet, Jose Luis Rosa

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000784

The Bifidobacterium dentium Bd1 Genome Sequence Reflects Its Genetic Adaptation to the Human Oral Cavity

Marco Ventura, Francesca Turroni, Aldert Zomer, Elena Foroni, Vanessa Giubellini, Francesca Bottacini, Carlos Canchaya, Marcus J. Claesson, Fei He, Maria Mantzourani, Laura Mulas, Alberto Ferrarini, Beile Gao, Massimo Delledonne, Bernard Henrissat, Pedro Coutinho, Marco Oggioni, Radhey S. Gupta, Ziding Zhang, David Beighton, Gerald F. Fitzgerald, Paul W. O'Toole, Douwe van Sinderen

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000785

Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs

Rachel A. F. Wozniak, Derrick E. Fouts, Matteo Spagnoletti, Mauro M. Colombo, Daniela Ceccarelli, Geneviève Garriss, Christine Déry, Vincent Burrus, Matthew K. Waldor

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000786

A Constant Light-Genetic Screen Identifies KISMET as a Regulator of Circadian Photoresponses

Raphaëlle Dubruille, Alejandro Murad, Michael Rosbash, Patrick Emery

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000787

Feedback Inhibition in the PhoQ/PhoP Signaling System by a Membrane Peptide

Andrew M. Lippa, Mark Goulian

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000788

TGF-ß Sma/Mab Signaling Mutations Uncouple Reproductive Aging from Somatic Aging

Shijing Luo, Wendy M. Shaw, Jasmine Ashraf, Coleen T. Murphy

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000789

The Human Retinoblastoma Gene Is Imprinted

Deniz Kanber, Tea Berulava, Ole Ammerpohl, Diana Mitter, Julia Richter, Reiner Siebert, Bernhard Horsthemke, Dietmar Lohmann, Karin Buiting

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000790

Common Genetic Variation and the Control of HIV-1 in Humans

Jacques Fellay, Dongliang Ge, Kevin V. Shianna, Sara Colombo, Bruno Ledergerber, Elizabeth T. Cirulli, Thomas J. Urban, Kunlin Zhang, Curtis E. Gumbs, Jason P. Smith, Antonella Castagna, Alessandro Cozzi-Lepri, Andrea De Luca, Philippa Easterbrook, Huldrych F. Günthard, Simon Mallal, Cristina Mussini, Judith Dalmau, Javier Martinez-Picado, José M. Miro, Niels Obel, Steven M. Wolinsky, Jeremy J. Martinson, Roger Detels, Joseph B. Margolick, Lisa P. Jacobson, Patrick Descombes, Stylianos E. Antonarakis, Jacques S. Beckmann, Stephen J. O'Brien, Norman L. Letvin, Andrew J. McMichael, Barton F. Haynes, Mary Carrington, Sheng Feng, Amalio Telenti, David B. Goldstein, NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI)

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000791

Autoimmune Disease Classification by Inverse Association with SNP Alleles

Marina Sirota, Marc A. Schaub, Serafim Batzoglou, William H. Robinson, Atul J. Butte

PLOS Genetics: published December 24, 2009 | https://doi.org/10.1371/journal.pgen.1000792

Alternative Splicing Events Are a Late Feature of Pathology in a Mouse Model of Spinal Muscular Atrophy

Dirk Bäumer, Sheena Lee, George Nicholson, Joanna L. Davies, Nicholas J. Parkinson, Lyndsay M. Murray, Thomas H. Gillingwater, Olaf Ansorge, Kay E. Davies, Kevin Talbot

PLOS Genetics: published December 18, 2009 | https://doi.org/10.1371/journal.pgen.1000773

Mobile Antibiotic Resistance Encoding Elements Promote Their Own Diversity

Geneviève Garriss, Matthew K. Waldor, Vincent Burrus

PLOS Genetics: published December 18, 2009 | https://doi.org/10.1371/journal.pgen.1000775

Aging Mice Show a Decreasing Correlation of Gene Expression within Genetic Modules

Lucinda K. Southworth, Art B. Owen, Stuart K. Kim

PLOS Genetics: published December 18, 2009 | https://doi.org/10.1371/journal.pgen.1000776

Fruit-Surface Flavonoid Accumulation in Tomato Is Controlled by a SlMYB12-Regulated Transcriptional Network

Avital Adato, Tali Mandel, Shira Mintz-Oron, Ilya Venger, Dorit Levy, Merav Yativ, Eva Domínguez, Zhonghua Wang, Ric C. H. De Vos, Reinhard Jetter, Lukas Schreiber, Antonio Heredia, Ilana Rogachev, Asaph Aharoni

PLOS Genetics: published December 18, 2009 | https://doi.org/10.1371/journal.pgen.1000777

DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

Peter C. Hollenhorst, Katherine J. Chandler, Rachel L. Poulsen, W. Evan Johnson, Nancy A. Speck, Barbara J. Graves

PLOS Genetics: published December 18, 2009 | https://doi.org/10.1371/journal.pgen.1000778

Epigenetic Control of Virulence Gene Expression in Pseudomonas aeruginosa by a LysR-Type Transcription Regulator

Keith H. Turner, Isabelle Vallet-Gely, Simon L. Dove

PLOS Genetics: published December 18, 2009 | https://doi.org/10.1371/journal.pgen.1000779

The Dystrophin Complex Controls BK Channel Localization and Muscle Activity in Caenorhabditis elegans

Hongkyun Kim, Jonathan T. Pierce-Shimomura, Hyun J. Oh, Brandon E. Johnson, Miriam B. Goodman, Steven L. McIntire

PLOS Genetics: published December 18, 2009 | https://doi.org/10.1371/journal.pgen.1000780

A Mouse Model of the Human Fragile X Syndrome I304N Mutation

Julie B. Zang, Elena D. Nosyreva, Corinne M. Spencer, Lenora J. Volk, Kiran Musunuru, Ru Zhong, Elizabeth F. Stone, Lisa A. Yuva-Paylor, Kimberly M. Huber, Richard Paylor, Jennifer C. Darnell, Robert B. Darnell

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000758

Discovery of Candidate Disease Genes in ENU–Induced Mouse Mutants by Large-Scale Sequencing, Including a Splice-Site Mutation in Nucleoredoxin

Melissa K. Boles, Bonney M. Wilkinson, Laurens G. Wilming, Bin Liu, Frank J. Probst, Jennifer Harrow, Darren Grafham, Kathryn E. Hentges, Lanette P. Woodward, Andrea Maxwell, Karen Mitchell, Michael D. Risley, Randy Johnson, Karen Hirschi, James R. Lupski, Yosuke Funato, Hiroaki Miki, Pablo Marin-Garcia, Lucy Matthews, Alison J. Coffey, Anne Parker, Tim J. Hubbard, Jane Rogers, Allan Bradley, David J. Adams, Monica J. Justice

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000759

SOS Response Induces Persistence to Fluoroquinolones in Escherichia coli

Tobias Dörr, Kim Lewis, Marin Vulić

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000760

Regulators of AWC-Mediated Olfactory Plasticity in Caenorhabditis elegans

Damien M. O'Halloran, Svetlana Altshuler-Keylin, Jin I. Lee, Noelle D. L'Etoile

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000761

Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates

Gayle K. McEwen, Debbie K. Goode, Hugo J. Parker, Adam Woolfe, Heather Callaway, Greg Elgar

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000762

Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice

Alexei A. Aravin, Godfried W. van der Heijden, Julio Castañeda, Vasily V. Vagin, Gregory J. Hannon, Alex Bortvin

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000764

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Fine-Scale Variation and Genetic Determinants of Alternative Splicing across Individuals

Jasmin Coulombe-Huntington, Kevin C. L. Lam, Christel Dias, Jacek Majewski

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000766

Comprehensive Functional Analysis of Mycobacterium tuberculosis Toxin-Antitoxin Systems: Implications for Pathogenesis, Stress Responses, and Evolution

Holly R. Ramage, Lynn E. Connolly, Jeffery S. Cox

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000767

A Genome-Wide Association Study Reveals Variants in ARL15 that Influence Adiponectin Levels

J. Brent Richards, Dawn Waterworth, Stephen O'Rahilly, Marie-France Hivert, Ruth J. F. Loos, John R. B. Perry, Toshiko Tanaka, Nicholas John Timpson, Robert K. Semple, Nicole Soranzo, Kijoung Song, Nuno Rocha, Elin Grundberg, Josée Dupuis, Jose C. Florez, Claudia Langenberg, Inga Prokopenko, Richa Saxena, Robert Sladek, Yurii Aulchenko, David Evans, Gerard Waeber, Jeanette Erdmann, Mary-Susan Burnett, Naveed Sattar, Joseph Devaney, Christina Willenborg, Aroon Hingorani, Jaquelin C. M. Witteman, Peter Vollenweider, Beate Glaser, Christian Hengstenberg, Luigi Ferrucci, David Melzer, Klaus Stark, John Deanfield, Janina Winogradow, Martina Grassl, Alistair S. Hall, Josephine M. Egan, John R. Thompson, Sally L. Ricketts, Inke R. König, Wibke Reinhard, Scott Grundy, H-Erich Wichmann, Phil Barter, Robert Mahley, Y. Antero Kesaniemi, Daniel J. Rader, Muredach P. Reilly, Stephen E. Epstein, Alexandre F. R. Stewart, Cornelia M. Van Duijn, Heribert Schunkert, Keith Burling, Panos Deloukas, Tomi Pastinen, Nilesh J. Samani, Ruth McPherson, George Davey Smith, Timothy M. Frayling, Nicholas J. Wareham, James B. Meigs, Vincent Mooser, Tim D. Spector, GIANT Consortium

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000768

Interaction of HP1 and Brg1/Brm with the Globular Domain of Histone H3 Is Required for HP1-Mediated Repression

Marc Lavigne, Ragnhild Eskeland, Saliha Azebi, Violaine Saint-André, Suk Min Jang, Eric Batsché, Hua-Ying Fan, Robert E. Kingston, Axel Imhof, Christian Muchardt

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000769

The Synaptonemal Complex Protein Zip1 Promotes Bi-Orientation of Centromeres at Meiosis I

Mara N. Gladstone, David Obeso, Hoa Chuong, Dean S. Dawson

PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000771

Network Properties of Robust Immunity in Plants

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PLOS Genetics: published December 11, 2009 | https://doi.org/10.1371/journal.pgen.1000772

Stoichiometry of Base Excision Repair Proteins Correlates with Increased Somatic CAG Instability in Striatum over Cerebellum in Huntington's Disease Transgenic Mice

Agathi-Vassiliki Goula, Brian R. Berquist, David M. Wilson III, Vanessa C. Wheeler, Yvon Trottier, Karine Merienne

PLOS Genetics: published December 4, 2009 | https://doi.org/10.1371/journal.pgen.1000749

Severe Osteogenesis Imperfecta in Cyclophilin B–Deficient Mice

Jae Won Choi, Shari L. Sutor, Lonn Lindquist, Glenda L. Evans, Benjamin J. Madden, H. Robert Bergen III, Theresa E. Hefferan, Michael J. Yaszemski, Richard J. Bram

PLOS Genetics: published December 4, 2009 | https://doi.org/10.1371/journal.pgen.1000750

Dosage Regulation of the Active X Chromosome in Human Triploid Cells

Xinxian Deng, Di Kim Nguyen, R. Scott Hansen, Daniel L. Van Dyke, Stanley M. Gartler, Christine M. Disteche

PLOS Genetics: published December 4, 2009 | https://doi.org/10.1371/journal.pgen.1000751

Pparγ2 Is a Key Driver of Longevity in the Mouse

Carmen Argmann, Radu Dobrin, Sami Heikkinen, Aurélie Auburtin, Laurent Pouilly, Terrie-Anne Cock, Hana Koutnikova, Jun Zhu, Eric E. Schadt, Johan Auwerx

PLOS Genetics: published December 4, 2009 | https://doi.org/10.1371/journal.pgen.1000752

Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

Peter L. Oliver, Leo Goodstadt, Joshua J. Bayes, Zoë Birtle, Kevin C. Roach, Nitin Phadnis, Scott A. Beatson, Gerton Lunter, Harmit S. Malik, Chris P. Ponting

PLOS Genetics: published December 4, 2009 | https://doi.org/10.1371/journal.pgen.1000753

Multi-Organ Expression Profiling Uncovers a Gene Module in Coronary Artery Disease Involving Transendothelial Migration of Leukocytes and LIM Domain Binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) Study

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The Origin Recognition Complex Interacts with a Subset of Metabolic Genes Tightly Linked to Origins of Replication

Erika Shor, Christopher L. Warren, Joshua Tietjen, Zhonggang Hou, Ulrika Müller, Ilaria Alborelli, Florence H. Gohard, Adrian I. Yemm, Lev Borisov, James R. Broach, Michael Weinreich, Conrad A. Nieduszynski, Aseem Z. Ansari, Catherine A. Fox

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New Evidence Confirms That the Mitochondrial Bottleneck Is Generated without Reduction of Mitochondrial DNA Content in Early Primordial Germ Cells of Mice

Liqin Cao, Hiroshi Shitara, Michihiko Sugimoto, Jun-Ichi Hayashi, Kuniya Abe, Hiromichi Yonekawa

PLOS Genetics: published December 4, 2009 | https://doi.org/10.1371/journal.pgen.1000756

Homeobox Transcription Factors Are Required for Conidiation and Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae

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