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Table of Contents: March 2011

COVER

Image Credit: Hajime Watanabe
Issue Image
Female adult of the water flea Daphnia magna.

Daphnia magna is a freshwater crustacean. Normal, healthy populations are entirely parthenogenetic female. However, decline in environmental quality of the habitat leads to the clonal production of males, which allows sexual reproduction. This is known as environmental sex determination (see Kato et al., 10.1371/journal.pgen.1001345).

Viewpoints

Perspective

Review

Research Articles

SUMO-Targeted Ubiquitin Ligase, Rad60, and Nse2 SUMO Ligase Suppress Spontaneous Top1–Mediated DNA Damage and Genome Instability

Johanna Heideker, John Prudden, J. Jefferson P. Perry, John A. Tainer, Michael N. Boddy

Initial Mutations Direct Alternative Pathways of Protein Evolution

Merijn L. M. Salverda, Eynat Dellus, Florien A. Gorter, Alfons J. M. Debets, John van der Oost, Rolf F. Hoekstra, Dan S. Tawfik, J. Arjan G. M. de Visser

Testing for an Unusual Distribution of Rare Variants

Benjamin M. Neale, Manuel A. Rivas, Benjamin F. Voight, David Altshuler, Bernie Devlin, Marju Orho-Melander, Sekar Kathiresan, Shaun M. Purcell, Kathryn Roeder, Mark J. Daly

Differential Genetic Associations for Systemic Lupus Erythematosus Based on Anti–dsDNA Autoantibody Production

Sharon A. Chung, Kimberly E. Taylor, Robert R. Graham, Joanne Nititham, Annette T. Lee, Ward A. Ortmann, Chaim O. Jacob, Marta E. Alarcón-Riquelme, Betty P. Tsao, John B. Harley, Patrick M. Gaffney, Kathy L. Moser, Michelle Petri, F. Yesim Demirci, M. Ilyas Kamboh, Susan Manzi, Peter K. Gregersen, Carl D. Langefeld, Timothy W. Behrens, Lindsey A. Criswell , SLEGEN

Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches

Ghia M. Euskirchen, Raymond K. Auerbach, Eugene Davidov, Tara A. Gianoulis, Guoneng Zhong, Joel Rozowsky, Nitin Bhardwaj, Mark B. Gerstein, Michael Snyder

A Bow-Tie Genetic Architecture for Morphogenesis Suggested by a Genome-Wide RNAi Screen in Caenorhabditis elegans

Matthew D. Nelson, Elinor Zhou, Karin Kiontke, Hélène Fradin, Grayson Maldonado, Daniel Martin, Khushbu Shah, David H. A. Fitch

FUS Transgenic Rats Develop the Phenotypes of Amyotrophic Lateral Sclerosis and Frontotemporal Lobar Degeneration

Cao Huang, Hongxia Zhou, Jianbin Tong, Han Chen, Yong-Jian Liu, Dian Wang, Xiaotao Wei, Xu-Gang Xia

Polycomb Repressive Complex 2 Controls the Embryo-to-Seedling Phase Transition

Daniel Bouyer, Francois Roudier, Maren Heese, Ellen D. Andersen, Delphine Gey, Moritz K. Nowack, Justin Goodrich, Jean-Pierre Renou, Paul E. Grini, Vincent Colot, Arp Schnittger

Genome-Wide Association Analysis Identifies Variants Associated with Nonalcoholic Fatty Liver Disease That Have Distinct Effects on Metabolic Traits

Elizabeth K. Speliotes, Laura M. Yerges-Armstrong, Jun Wu, Ruben Hernaez, Lauren J. Kim, Cameron D. Palmer, Vilmundur Gudnason, Gudny Eiriksdottir, Melissa E. Garcia, Lenore J. Launer, Michael A. Nalls, Jeanne M. Clark, Braxton D. Mitchell, Alan R. Shuldiner, Johannah L. Butler, Marta Tomas, Udo Hoffmann, Shih-Jen Hwang, Joseph M. Massaro, Christopher J. O'Donnell, Dushyant V. Sahani, Veikko Salomaa, Eric E. Schadt, Stephen M. Schwartz, David S. Siscovick, Benjamin F. Voight, J. Jeffrey Carr, Mary F. Feitosa, Tamara B. Harris, Caroline S. Fox, Albert V. Smith, W. H. Linda Kao, Joel N. Hirschhorn, Ingrid B. Borecki , NASH CRN, GIANT Consortium, MAGIC Investigators, GOLD Consortium

The SUVR4 Histone Lysine Methyltransferase Binds Ubiquitin and Converts H3K9me1 to H3K9me3 on Transposon Chromatin in Arabidopsis

Silje V. Veiseth, Mohummad A. Rahman, Kyoko L. Yap, Andreas Fischer, Wolfgang Egge-Jacobsen, Gunter Reuter, Ming-Ming Zhou, Reidunn B. Aalen, Tage Thorstensen

A Cholinergic-Regulated Circuit Coordinates the Maintenance and Bi-Stable States of a Sensory-Motor Behavior during Caenorhabditis elegans Male Copulation

Yishi Liu, Brigitte LeBeouf, Xiaoyan Guo, Paola A. Correa, Daisy G. Gualberto, Robyn Lints, L. Rene Garcia

Global Analysis of the Relationship between JIL-1 Kinase and Transcription

Catherine Regnard, Tobias Straub, Angelika Mitterweger, Ina K. Dahlsveen, Viola Fabian, Peter B. Becker

Identification of a Novel Type of Spacer Element Required for Imprinting in Fission Yeast

Suha Sayrac, Sonya Vengrova, Emma L. Godfrey, Jacob Z. Dalgaard

Chiasmata Promote Monopolar Attachment of Sister Chromatids and Their Co-Segregation toward the Proper Pole during Meiosis I

Yukinobu Hirose, Ren Suzuki, Tatsunori Ohba, Yumi Hinohara, Hirotada Matsuhara, Masashi Yoshida, Yuta Itabashi, Hiroshi Murakami, Ayumu Yamamoto

Global Developmental Gene Expression and Pathway Analysis of Normal Brain Development and Mouse Models of Human Neuronal Migration Defects

Tiziano Pramparo, Ondrej Libiger, Sonia Jain, Hong Li, Yong Ha Youn, Shinji Hirotsune, Nicholas J. Schork, Anthony Wynshaw-Boris

Replicative Age Induces Mitotic Recombination in the Ribosomal RNA Gene Cluster of Saccharomyces cerevisiae

Derek L. Lindstrom, Christina K. Leverich, Kiersten A. Henderson, Daniel E. Gottschling

Rif1 Supports the Function of the CST Complex in Yeast Telomere Capping

Savani Anbalagan, Diego Bonetti, Giovanna Lucchini, Maria Pia Longhese

Phenotype Restricted Genome-Wide Association Study Using a Gene-Centric Approach Identifies Three Low-Risk Neuroblastoma Susceptibility Loci

Lễ B. Nguyễn, Sharon J. Diskin, Mario Capasso, Kai Wang, Maura A. Diamond, Joseph Glessner, Cecilia Kim, Edward F. Attiyeh, Yael P. Mosse, Kristina Cole, Achille Iolascon, Marcella Devoto, Hakon Hakonarson, Hongzhe K. Li, John M. Maris

A Novel Unstable Duplication Upstream of HAS2 Predisposes to a Breed-Defining Skin Phenotype and a Periodic Fever Syndrome in Chinese Shar-Pei Dogs

Mia Olsson, Jennifer R. S. Meadows, Katarina Truvé, Gerli Rosengren Pielberg, Francesca Puppo, Evan Mauceli, Javier Quilez, Noriko Tonomura, Giordana Zanna, Maria José Docampo, Anna Bassols, Anne C. Avery, Elinor K. Karlsson, Anne Thomas, Daniel L. Kastner, Erik Bongcam-Rudloff, Matthew T. Webster, Armand Sanchez, Åke Hedhammar, Elaine F. Remmers, Leif Andersson, Lluis Ferrer, Linda Tintle, Kerstin Lindblad-Toh

A Genome-Wide Association Study of Upper Aerodigestive Tract Cancers Conducted within the INHANCE Consortium

James D. McKay, Therese Truong, Valerie Gaborieau, Amelie Chabrier, Shu-Chun Chuang, Graham Byrnes, David Zaridze, Oxana Shangina, Neonila Szeszenia-Dabrowska, Jolanta Lissowska, Peter Rudnai, Eleonora Fabianova, Alexandru Bucur, Vladimir Bencko, Ivana Holcatova, Vladimir Janout, Lenka Foretova, Pagona Lagiou, Dimitrios Trichopoulos, Simone Benhamou, Christine Bouchardy, Wolfgang Ahrens, Franco Merletti, Lorenzo Richiardi, Renato Talamini, Luigi Barzan, Kristina Kjaerheim, Gary J. Macfarlane, Tatiana V. Macfarlane, Lorenzo Simonato, Cristina Canova, Antonio Agudo, Xavier Castellsagué, Ray Lowry, David I. Conway, Patricia A. McKinney, Claire M. Healy, Mary E. Toner, Ariana Znaor, Maria Paula Curado, Sergio Koifman, Ana Menezes, Victor Wünsch-Filho, José Eluf Neto, Leticia Fernández Garrote, Stefania Boccia, Gabriella Cadoni, Dario Arzani, Andrew F. Olshan, Mark C. Weissler, William K. Funkhouser, Jingchun Luo, Jan Lubiński, Joanna Trubicka, Marcin Lener, Dorota Oszutowska, Stephen M. Schwartz, Chu Chen, Sherianne Fish, David R. Doody, Joshua E. Muscat, Philip Lazarus, Carla J. Gallagher, Shen-Chih Chang, Zuo-Feng Zhang, Qingyi Wei, Erich M. Sturgis, Li-E Wang, Silvia Franceschi, Rolando Herrero, Karl T. Kelsey, Michael D. McClean, Carmen J. Marsit, Heather H. Nelson, Marjorie Romkes, Shama Buch, Tomoko Nukui, Shilong Zhong, Martin Lacko, Johannes J. Manni, Wilbert H. M. Peters, Rayjean J. Hung, John McLaughlin, Lars Vatten, Inger Njølstad, Gary E. Goodman, John K. Field, Triantafillos Liloglou, Paolo Vineis, Francoise Clavel-Chapelon, Domenico Palli, Rosario Tumino, Vittorio Krogh, Salvatore Panico, Carlos A. González, J. Ramón Quirós, Carmen Martínez, Carmen Navarro, Eva Ardanaz, Nerea Larrañaga, Kay-Tee Khaw, Timothy Key, H. Bas Bueno-de-Mesquita, Petra H. M. Peeters, Antonia Trichopoulou, Jakob Linseisen, Heiner Boeing, Göran Hallmans, Kim Overvad, Anne Tjønneland, Merethe Kumle, Elio Riboli, Kristjan Välk, Tõnu Voodern, Andres Metspalu, Diana Zelenika, Anne Boland, Marc Delepine, Mario Foglio, Doris Lechner, Hélène Blanché, Ivo G. Gut, Pilar Galan, Simon Heath, Mia Hashibe, Richard B. Hayes, Paolo Boffetta, Mark Lathrop, Paul Brennan

The FUN30 Chromatin Remodeler, Fft3, Protects Centromeric and Subtelomeric Domains from Euchromatin Formation

Annelie Strålfors, Julian Walfridsson, Hasanuzzaman Bhuiyan, Karl Ekwall

Role of the Drosophila Non-Visual ß-Arrestin Kurtz in Hedgehog Signalling

Cristina Molnar, Ana Ruiz-Gómez, Mercedes Martín, Susana Rojo-Berciano, Federico Mayor Jr., Jose F. de Celis

Quantifying the Underestimation of Relative Risks from Genome-Wide Association Studies

Chris Spencer, Eliana Hechter, Damjan Vukcevic, Peter Donnelly

Genome-Wide Interaction-Based Association Analysis Identified Multiple New Susceptibility Loci for Common Diseases

Yang Liu, Haiming Xu, Suchao Chen, Xianfeng Chen, Zhenguo Zhang, Zhihong Zhu, Xueying Qin, Landian Hu, Jun Zhu, Guo-Ping Zhao, Xiangyin Kong

Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability

Fausto Arellano-Carbajal, Luis Briseño-Roa, Africa Couto, Benny H. H. Cheung, Michel Labouesse, Mario de Bono

A Molecular Phylogeny of Living Primates

Polina Perelman, Warren E. Johnson, Christian Roos, Hector N. Seuánez, Julie E. Horvath, Miguel A. M. Moreira, Bailey Kessing, Joan Pontius, Melody Roelke, Yves Rumpler, Maria Paula C. Schneider, Artur Silva, Stephen J. O'Brien, Jill Pecon-Slattery

Viral Genome Segmentation Can Result from a Trade-Off between Genetic Content and Particle Stability

Samuel Ojosnegros, Juan García-Arriaza, Cristina Escarmís, Susanna C. Manrubia, Celia Perales, Armando Arias, Mauricio García Mateu, Esteban Domingo

Interactions among Polycomb Domains Are Guided by Chromosome Architecture

Bas Tolhuis, Marleen Blom, Ron M. Kerkhoven, Ludo Pagie, Hans Teunissen, Marja Nieuwland, Marieke Simonis, Wouter de Laat, Maarten van Lohuizen, Bas van Steensel

Histidine Protects Against Zinc and Nickel Toxicity in Caenorhabditis elegans

John T. Murphy, Janelle J. Bruinsma, Daniel L. Schneider, Sara Collier, James Guthrie, Asif Chinwalla, J. David Robertson, Elaine R. Mardis, Kerry Kornfeld

Whole-Exome Re-Sequencing in a Family Quartet Identifies POP1 Mutations As the Cause of a Novel Skeletal Dysplasia

Evgeny A. Glazov, Andreas Zankl, Marina Donskoi, Tony J. Kenna, Gethin P. Thomas, Graeme R. Clark, Emma L. Duncan, Matthew A. Brown

Ultra-Deep Sequencing of Mouse Mitochondrial DNA: Mutational Patterns and Their Origins

Adam Ameur, James B. Stewart, Christoph Freyer, Erik Hagström, Max Ingman, Nils-Göran Larsson, Ulf Gyllensten

Dopamine Signalling in Mushroom Bodies Regulates Temperature-Preference Behaviour in Drosophila

Sunhoe Bang, Seogang Hyun, Sung-Tae Hong, Jongkyun Kang, Kyunghwa Jeong, Joong-Jean Park, Joonho Choe, Jongkyeong Chung

Uncoupling Antisense-Mediated Silencing and DNA Methylation in the Imprinted Gnas Cluster

Christine M. Williamson, Simon T. Ball, Claire Dawson, Stuti Mehta, Colin V. Beechey, Martin Fray, Lydia Teboul, T. Neil Dear, Gavin Kelsey, Jo Peters

Systematic Detection of Polygenic cis-Regulatory Evolution

Hunter B. Fraser, Tomas Babak, John Tsang, Yiqi Zhou, Bin Zhang, Margarete Mehrabian, Eric E. Schadt

REVEILLE8 and PSEUDO-REPONSE REGULATOR5 Form a Negative Feedback Loop within the Arabidopsis Circadian Clock

Reetika Rawat, Nozomu Takahashi, Polly Yingshan Hsu, Matthew A. Jones, Jacob Schwartz, Michelle R. Salemi, Brett S. Phinney, Stacey L. Harmer

Cancer-Associated Splicing Variant of Tumor Suppressor AIMP2/p38: Pathological Implication in Tumorigenesis

Jin Woo Choi, Dae Gyu Kim, Al-Eum Lee, Hye Rim Kim, Jin Young Lee, Nam Hoon Kwon, Young Kee Shin, Soon-Kyung Hwang, Seung-Hee Chang, Myung-Haing Cho, Yoon-La Choi, Jhingook Kim, Seung Hyun Oh, Bora Kim, Soo-Youl Kim, Hyo-Sung Jeon, Jae Yong Park, Hyunseok Peter Kang, Bum Joon Park, Jung Min Han, Sunghoon Kim

Ancestral Mutation in Telomerase Causes Defects in Repeat Addition Processivity and Manifests As Familial Pulmonary Fibrosis

Jonathan K. Alder, Joy D. Cogan, Andrew F. Brown, Collin J. Anderson, William E. Lawson, Peter M. Lansdorp, John A. Phillips III, James E. Loyd, Julian J.-L. Chen, Mary Armanios

H3 Lysine 4 Is Acetylated at Active Gene Promoters and Is Regulated by H3 Lysine 4 Methylation

Benoit Guillemette, Paul Drogaris, Hsiu-Hsu Sophia Lin, Harry Armstrong, Kyoko Hiragami-Hamada, Axel Imhof, Éric Bonneil, Pierre Thibault, Alain Verreault, Richard J. Festenstein

Widespread Hypomethylation Occurs Early and Synergizes with Gene Amplification during Esophageal Carcinogenesis

Hector Alvarez, Joanna Opalinska, Li Zhou, Davendra Sohal, Melissa J. Fazzari, Yiting Yu, Christina Montagna, Elizabeth A. Montgomery, Marcia Canto, Kerry B. Dunbar, Jean Wang, Juan Carlos Roa, Yongkai Mo, Tushar Bhagat, K. H. Ramesh, Linda Cannizzaro, J. Mollenhauer, Reid F. Thompson, Masako Suzuki, Stephen Meltzer, Ari Melnick, John M. Greally, Anirban Maitra, Amit Verma

Roles of brca2 (fancd1) in Oocyte Nuclear Architecture, Gametogenesis, Gonad Tumors, and Genome Stability in Zebrafish

Adriana Rodríguez-Marí, Catherine Wilson, Tom A. Titus, Cristian Cañestro, Ruth A. BreMiller, Yi-Lin Yan, Indrajit Nanda, Adam Johnston, John P. Kanki, Erin M. Gray, Xinjun He, Jan Spitsbergen, Detlev Schindler, John H. Postlethwait

ARGONAUTE10 and ARGONAUTE1 Regulate the Termination of Floral Stem Cells through Two MicroRNAs in Arabidopsis

Lijuan Ji, Xigang Liu, Jun Yan, Wenming Wang, Rae Eden Yumul, Yun Ju Kim, Thanh Theresa Dinh, Jun Liu, Xia Cui, Binglian Zheng, Manu Agarwal, Chunyan Liu, Xiaofeng Cao, Guiliang Tang, Xuemei Chen

The Toll-Like Receptor Gene Family Is Integrated into Human DNA Damage and p53 Networks

Daniel Menendez, Maria Shatz, Kathleen Azzam, Stavros Garantziotis, Michael B. Fessler, Michael A. Resnick