January 2010

In this issue of PLoS Genetics, Wang et al. report a spontaneous pseudoviviparous mutant phoenix (pho) in rice. In pho plants, all spikelets are replaced by young plantlets, and the reproductive strategy is completely changed from sexual to asexual. Further analyses revealed that pho is caused by mutations of two MADS-box transcription factors. These findings provide an insight into the mechanism of pseudovivipary in plants.

Image Credit: Zhukuan Cheng (Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, China)

Interview

The Gift of Observation: An Interview with Mary Lyon

Jane Gitschier

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000813

Perspective

Rising from the Ashes: DNA Repair in Deinococcus radiodurans

Michael M. Cox, James L. Keck, John R. Battista

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000815

Research Articles

Genetic Crossovers Are Predicted Accurately by the Computed Human Recombination Map

Pavel P. Khil, R. Daniel Camerini-Otero

PLOS Genetics: published January 29, 2010 | https://doi.org/10.1371/journal.pgen.1000831

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line

Michael James Clark, Nils Homer, Brian D. O'Connor, Zugen Chen, Ascia Eskin, Hane Lee, Barry Merriman, Stanley F. Nelson

PLOS Genetics: published January 29, 2010 | https://doi.org/10.1371/journal.pgen.1000832

Elevated Levels of the Polo Kinase Cdc5 Override the Mec1/ATR Checkpoint in Budding Yeast by Acting at Different Steps of the Signaling Pathway

Roberto Antonio Donnianni, Matteo Ferrari, Federico Lazzaro, Michela Clerici, Benjamin Tamilselvan Nachimuthu, Paolo Plevani, Marco Muzi-Falconi, Achille Pellicioli

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000763

DEP and AFO Regulate Reproductive Habit in Rice

Kejian Wang, Ding Tang, Lilan Hong, Wenying Xu, Jian Huang, Ming Li, Minghong Gu, Yongbiao Xue, Zhukuan Cheng

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000818

Nonsense-Mediated Decay Enables Intron Gain in Drosophila

Ashley Farlow, Eshwar Meduri, Marlies Dolezal, Liushuai Hua, Christian Schlötterer

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000819

The Caenorhabditis elegans Elongator Complex Regulates Neuronal α-tubulin Acetylation

Jachen A. Solinger, Roberta Paolinelli, Holger Klöß, Francesco Berlanda Scorza, Stefano Marchesi, Ursula Sauder, Dai Mitsushima, Fabrizio Capuani, Stephen R. Stürzenbaum, Giuseppe Cassata

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000820

Environmental and Genetic Determinants of Colony Morphology in Yeast

Joshua A. Granek, Paul M. Magwene

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000823

Distinct Type of Transmission Barrier Revealed by Study of Multiple Prion Determinants of Rnq1

Michele L. Kadnar, Gulnara Articov, Irina L. Derkatch

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000824

Evidence for Pervasive Adaptive Protein Evolution in Wild Mice

Daniel L. Halligan, Fiona Oliver, Adam Eyre-Walker, Bettina Harr, Peter D. Keightley

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000825

BRIT1/MCPH1 Is Essential for Mitotic and Meiotic Recombination DNA Repair and Maintaining Genomic Stability in Mice

Yulong Liang, Hong Gao, Shiaw-Yih Lin, Guang Peng, Xingxu Huang, Pumin Zhang, John A. Goss, Francis C. Brunicardi, Asha S. Multani, Sandy Chang, Kaiyi Li

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000826

Collaborative Action of Brca1 and CtIP in Elimination of Covalent Modifications from Double-Strand Breaks to Facilitate Subsequent Break Repair

Kyoko Nakamura, Toshiaki Kogame, Hiroyuki Oshiumi, Akira Shinohara, Yoshiki Sumitomo, Keli Agama, Yves Pommier, Kimiko M. Tsutsui, Ken Tsutsui, Edgar Hartsuiker, Tomoo Ogi, Shunichi Takeda, Yoshihito Taniguchi

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000828

Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers

Richard W. Lusk, Michael B. Eisen

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000829

Differential Localization and Independent Acquisition of the H3K9me2 and H3K9me3 Chromatin Modifications in the Caenorhabditis elegans Adult Germ Line

Jessica B. Bessler, Erik C. Andersen, Anne M. Villeneuve

PLOS Genetics: published January 22, 2010 | https://doi.org/10.1371/journal.pgen.1000830

A Major Role of the RecFOR Pathway in DNA Double-Strand-Break Repair through ESDSA in Deinococcus radiodurans

Esma Bentchikou, Pascale Servant, Geneviève Coste, Suzanne Sommer

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000774

Irradiation-Induced Deinococcus radiodurans Genome Fragmentation Triggers Transposition of a Single Resident Insertion Sequence

Cécile Pasternak, Bao Ton-Hoang, Geneviève Coste, Adriana Bailone, Michael Chandler, Suzanne Sommer

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000799

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

Sara Vieira-Silva, Eduardo P. C. Rocha

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000808

Kidney Development in the Absence of Gdnf and Spry1 Requires Fgf10

Odyssé Michos, Cristina Cebrian, Deborah Hyink, Uta Grieshammer, Linda Williams, Vivette D'Agati, Jonathan D. Licht, Gail R. Martin, Frank Costantini

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000809

Co-Orientation of Replication and Transcription Preserves Genome Integrity

Anjana Srivatsan, Ashley Tehranchi, David M. MacAlpine, Jue D. Wang

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000810

Maternal Ethanol Consumption Alters the Epigenotype and the Phenotype of Offspring in a Mouse Model

Nina Kaminen-Ahola, Arttu Ahola, Murat Maga, Kylie-Ann Mallitt, Paul Fahey, Timothy C. Cox, Emma Whitelaw, Suyinn Chong

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000811

Altered Gene Expression and DNA Damage in Peripheral Blood Cells from Friedreich's Ataxia Patients: Cellular Model of Pathology

Astrid C. Haugen, Nicholas A. Di Prospero, Joel S. Parker, Rick D. Fannin, Jeff Chou, Joel N. Meyer, Christopher Halweg, Jennifer B. Collins, Alexandra Durr, Kenneth Fischbeck, Bennett Van Houten

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000812

A Comprehensive Map of Insulator Elements for the Drosophila Genome

Nicolas Nègre, Christopher D. Brown, Parantu K. Shah, Pouya Kheradpour, Carolyn A. Morrison, Jorja G. Henikoff, Xin Feng, Kami Ahmad, Steven Russell, Robert A. H. White, Lincoln Stein, Steven Henikoff, Manolis Kellis, Kevin P. White

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000814

Genetic Dissection of Differential Signaling Threshold Requirements for the Wnt/β-Catenin Pathway In Vivo

Michael Buchert, Dimitris Athineos, Helen E. Abud, Zoe D. Burke, Maree C. Faux, Michael S. Samuel, Andrew G. Jarnicki, Catherine E. Winbanks, Ian P. Newton, Valerie S. Meniel, Hiromu Suzuki, Steven A. Stacker, Inke S. Näthke, David Tosh, Joerg Huelsken, Alan R. Clarke, Joan K. Heath, Owen J. Sansom, Matthias Ernst

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000816

The MCM-Binding Protein ETG1 Aids Sister Chromatid Cohesion Required for Postreplicative Homologous Recombination Repair

Naoki Takahashi, Mauricio Quimbaya, Veit Schubert, Tim Lammens, Klaas Vandepoele, Ingo Schubert, Minami Matsui, Dirk Inzé, Geert Berx, Lieven De Veylder

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000817

Non-Coding Changes Cause Sex-Specific Wing Size Differences between Closely Related Species of Nasonia

David W. Loehlin, Deodoro C. S. G. Oliveira, Rachel Edwards, Jonathan D. Giebel, Michael E. Clark, M. Victoria Cattani, Louis van de Zande, Eveline C. Verhulst, Leo W. Beukeboom, Monica Muñoz-Torres, John H. Werren

PLOS Genetics: published January 15, 2010 | https://doi.org/10.1371/journal.pgen.1000821

Inverse Correlation between Promoter Strength and Excision Activity in Class 1 Integrons

Thomas Jové, Sandra Da Re, François Denis, Didier Mazel, Marie-Cécile Ploy

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000793

miR-30 Regulates Mitochondrial Fission through Targeting p53 and the Dynamin-Related Protein-1 Pathway

Jincheng Li, Stefan Donath, Yanrui Li, Danian Qin, Bellur S. Prabhakar, Peifeng Li

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000795

Genotype and Gene Expression Associations with Immune Function in Drosophila

Timothy B. Sackton, Brian P. Lazzaro, Andrew G. Clark

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000797

Modeling of Environmental Effects in Genome-Wide Association Studies Identifies SLC2A2 and HP as Novel Loci Influencing Serum Cholesterol Levels

Wilmar Igl, Åsa Johansson, James F. Wilson, Sarah H. Wild, Ozren Polašek, Caroline Hayward, Veronique Vitart, Nicholas Hastie, Pavao Rudan, Carsten Gnewuch, Gerd Schmitz, Thomas Meitinger, Peter P. Pramstaller, Andrew A. Hicks, Ben A. Oostra, Cornelia M. van Duijn, Igor Rudan, Alan Wright, Harry Campbell, Ulf Gyllensten, EUROSPAN Consortium

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000798

Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast

Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000800

The Caenorhabditis elegans Werner Syndrome Protein Functions Upstream of ATR and ATM in Response to DNA Replication Inhibition and Double-Strand DNA Breaks

Se-Jin Lee, Anton Gartner, Moonjung Hyun, Byungchan Ahn, Hyeon-Sook Koo

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000801

Mis-Spliced Transcripts of Nicotinic Acetylcholine Receptor α6 Are Associated with Field Evolved Spinosad Resistance in Plutella xylostella (L.)

Simon W. Baxter, Mao Chen, Anna Dawson, Jian-Zhou Zhao, Heiko Vogel, Anthony M. Shelton, David G. Heckel, Chris D. Jiggins

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000802

Postnatal Survival of Mice with Maternal Duplication of Distal Chromosome 7 Induced by a Igf2/H19 Imprinting Control Region Lacking Insulator Function

Li Han, Piroska E. Szabó, Jeffrey R. Mann

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000803

VEZF1 Elements Mediate Protection from DNA Methylation

Jacqueline Dickson, Humaira Gowher, Ruslan Strogantsev, Miklos Gaszner, Alan Hair, Gary Felsenfeld, Adam G. West

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000804

Alternative Epigenetic Chromatin States of Polycomb Target Genes

Yuri B. Schwartz, Tatyana G. Kahn, Per Stenberg, Katsuhito Ohno, Richard Bourgon, Vincenzo Pirrotta

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000805

Genome-Wide Association Study Identifies ALDH7A1 as a Novel Susceptibility Gene for Osteoporosis

Yan Guo, Li-Jun Tan, Shu-Feng Lei, Tie-Lin Yang, Xiang-Ding Chen, Feng Zhang, Yuan Chen, Feng Pan, Han Yan, Xiaogang Liu, Qing Tian, Zhi-Xin Zhang, Qi Zhou, Chuan Qiu, Shan-Shan Dong, Xiang-Hong Xu, Yan-Fang Guo, Xue-Zhen Zhu, Shan-Lin Liu, Xiang-Li Wang, Xi Li, Yi Luo, Li-Shu Zhang, Meng Li, Jin-Tang Wang, Ting Wen, Betty Drees, James Hamilton, Christopher J. Papasian, Robert R. Recker, Xiao-Ping Song, Jing Cheng, Hong-Wen Deng

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000806

Activation of Mutant Enzyme Function In Vivo by Proteasome Inhibitors and Treatments that Induce Hsp70

Laishram R. Singh, Sapna Gupta, Nicholaas H. Honig, Jan P. Kraus, Warren D. Kruger

PLOS Genetics: published January 8, 2010 | https://doi.org/10.1371/journal.pgen.1000807

Cover

A panicle of the rice pseudoviviparous mutant shows that all spikelets are replaced by vigorous juvenile plantlets.

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