June 2011

Millions of pollen grains are ready to fertilize the ovules of ears of maize. This is easy to control because male flowers on the top (tassel as seen) and female flowers on the side (ears) are physically separated, allowing either self- or hybrid crosses, which has advanced breeding in agriculture and made maize the highest yielding grain. To further enable the improvement of grain quality, Miclaus et al. studied the architecture, expression, and epiregulation of a medium-size gene family, the alpha-zeins, in two maize haplotypes, B73 and BSSS53.

Image Credit: Mihai Miclaus (Waksman Institute of Microbiology)

Interview

Vive La Différence: An Interview with Catherine Dulac

Jane Gitschier

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002140

Viewpoints

Statistical Inference on the Mechanisms of Genome Evolution

Michael Lynch

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1001389

Drift and Genome Complexity Revisited

Kenneth D. Whitney, Bastien Boussau, Eric J. Baack, Theodore Garland Jr.

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002092

Perspective

Revisiting Heterochromatin in Embryonic Stem Cells

Irina Stancheva

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002093

Review

Chromosomal Macrodomains and Associated Proteins: Implications for DNA Organization and Replication in Gram Negative Bacteria

Remus T. Dame, Olga J. Kalmykowa, David C. Grainger

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002123

Research Articles

Identification of Nine Novel Loci Associated with White Blood Cell Subtypes in a Japanese Population

Yukinori Okada, Tomomitsu Hirota, Yoichiro Kamatani, Atsushi Takahashi, Hiroko Ohmiya, Natsuhiko Kumasaka, Koichiro Higasa, Yumi Yamaguchi-Kabata, Naoya Hosono, Michael A. Nalls, Ming Huei Chen, Frank J. A. van Rooij, Albert V. Smith, Toshiko Tanaka, David J. Couper, Neil A. Zakai, Luigi Ferrucci, Dan L. Longo, Dena G. Hernandez, Jacqueline C. M. Witteman, Tamara B. Harris, Christopher J. O'Donnell, Santhi K. Ganesh, Koichi Matsuda, Tatsuhiko Tsunoda, Toshihiro Tanaka, Michiaki Kubo, Yusuke Nakamura, Mayumi Tamari, Kazuhiko Yamamoto, Naoyuki Kamatani

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002067

Genome-Wide Association Study of White Blood Cell Count in 16,388 African Americans: the Continental Origins and Genetic Epidemiology Network (COGENT)

Alexander P. Reiner, Guillaume Lettre, Michael A. Nalls, Santhi K. Ganesh, Rasika Mathias, Melissa A. Austin, Eric Dean, Sampath Arepalli, Angela Britton, Zhao Chen, David Couper, J. David Curb, Charles B. Eaton, Myriam Fornage, Struan F. A. Grant, Tamara B. Harris, Dena Hernandez, Naoyuki Kamatini, Brendan J. Keating, Michiaki Kubo, Andrea LaCroix, Leslie A. Lange, Simin Liu, Kurt Lohman, Yan Meng, Emile R. Mohler III, Solomon Musani, Yusuke Nakamura, Christopher J. O'Donnell, Yukinori Okada, Cameron D. Palmer, George J. Papanicolaou, Kushang V. Patel, Andrew B. Singleton, Atsushi Takahashi, Hua Tang, Herman A. Taylor Jr., Kent Taylor, Cynthia Thomson, Lisa R. Yanek, Lingyao Yang, Elad Ziv, Alan B. Zonderman, Aaron R. Folsom, Michele K. Evans, Yongmei Liu, Diane M. Becker, Beverly M. Snively, James G. Wilson

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002108

Multiple Loci Are Associated with White Blood Cell Phenotypes

Michael A. Nalls, David J. Couper, Toshiko Tanaka, Frank J. A. van Rooij, Ming-Huei Chen, Albert V. Smith, Daniela Toniolo, Neil A. Zakai, Qiong Yang, Andreas Greinacher, Andrew R. Wood, Melissa Garcia, Paolo Gasparini, Yongmei Liu, Thomas Lumley, Aaron R. Folsom, Alex P. Reiner, Christian Gieger, Vasiliki Lagou, Janine F. Felix, Henry Völzke, Natalia A. Gouskova, Alessandro Biffi, Angela Döring, Uwe Völker, Sean Chong, Kerri L. Wiggins, Augusto Rendon, Abbas Dehghan, Matt Moore, Kent Taylor, James G. Wilson, Guillaume Lettre, Albert Hofman, Joshua C. Bis, Nicola Pirastu, Caroline S. Fox, Christa Meisinger, Jennifer Sambrook, Sampath Arepalli, Matthias Nauck, Holger Prokisch, Jonathan Stephens, Nicole L. Glazer, L. Adrienne Cupples, Yukinori Okada, Atsushi Takahashi, Yoichiro Kamatani, Koichi Matsuda, Tatsuhiko Tsunoda, Toshihiro Tanaka, Michiaki Kubo, Yusuke Nakamura, Kazuhiko Yamamoto, Naoyuki Kamatani, Michael Stumvoll, Anke Tönjes, Inga Prokopenko, Thomas Illig, Kushang V. Patel, Stephen F. Garner, Brigitte Kuhnel, Massimo Mangino, Ben A. Oostra, Swee Lay Thein, Josef Coresh, H.-Erich Wichmann, Stephan Menzel, JingPing Lin, Giorgio Pistis, André G. Uitterlinden, Tim D. Spector, Alexander Teumer, Gudny Eiriksdottir, Vilmundur Gudnason, Stefania Bandinelli, Timothy M. Frayling, Aravinda Chakravarti, Cornelia M. van Duijn, David Melzer, Willem H. Ouwehand, Daniel Levy, Eric Boerwinkle, Andrew B. Singleton, Dena G. Hernandez, Dan L. Longo, Nicole Soranzo, Jacqueline C. M. Witteman, Bruce M. Psaty, Luigi Ferrucci, Tamara B. Harris, Christopher J. O'Donnell, Santhi K. Ganesh

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002113

A Single Sex Pheromone Receptor Determines Chemical Response Specificity of Sexual Behavior in the Silkmoth Bombyx mori

Takeshi Sakurai, Hidefumi Mitsuno, Stephan Shuichi Haupt, Keiro Uchino, Fumio Yokohari, Takaaki Nishioka, Isao Kobayashi, Hideki Sezutsu, Toshiki Tamura, Ryohei Kanzaki

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002115

A Functional Variant in MicroRNA-146a Promoter Modulates Its Expression and Confers Disease Risk for Systemic Lupus Erythematosus

Xiaobing Luo, Wanling Yang, Dong-Qing Ye, Huijuan Cui, Yan Zhang, Nattiya Hirankarn, Xiaoxia Qian, Yuanjia Tang, Yu Lung Lau, Niek de Vries, Paul Peter Tak, Betty P. Tsao, Nan Shen

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002128

Genome-Wide Association of Bipolar Disorder Suggests an Enrichment of Replicable Associations in Regions near Genes

Erin N. Smith, Daniel L. Koller, Corrie Panganiban, Szabolcs Szelinger, Peng Zhang, Judith A. Badner, Thomas B. Barrett, Wade H. Berrettini, Cinnamon S. Bloss, William Byerley, William Coryell, Howard J. Edenberg, Tatiana Foroud, Elliot S. Gershon, Tiffany A. Greenwood, Yiran Guo, Maria Hipolito, Brendan J. Keating, William B. Lawson, Chunyu Liu, Pamela B. Mahon, Melvin G. McInnis, Francis J. McMahon, Rebecca McKinney, Sarah S. Murray, Caroline M. Nievergelt, John I. Nurnberger Jr., Evaristus A. Nwulia, James B. Potash, John Rice, Thomas G. Schulze, William A. Scheftner, Paul D. Shilling, Peter P. Zandi, Sebastian Zöllner, David W. Craig, Nicholas J. Schork, John R. Kelsoe

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002134

Genetic Determinants of Lipid Traits in Diverse Populations from the Population Architecture using Genomics and Epidemiology (PAGE) Study

Logan Dumitrescu, Cara L. Carty, Kira Taylor, Fredrick R. Schumacher, Lucia A. Hindorff, José L. Ambite, Garnet Anderson, Lyle G. Best, Kristin Brown-Gentry, Petra Bůžková, Christopher S. Carlson, Barbara Cochran, Shelley A. Cole, Richard B. Devereux, Dave Duggan, Charles B. Eaton, Myriam Fornage, Nora Franceschini, Jeff Haessler, Barbara V. Howard, Karen C. Johnson, Sandra Laston, Laurence N. Kolonel, Elisa T. Lee, Jean W. MacCluer, Teri A. Manolio, Sarah A. Pendergrass, Miguel Quibrera, Ralph V. Shohet, Lynne R. Wilkens, Christopher A. Haiman, Loïc Le Marchand, Steven Buyske, Charles Kooperberg, Kari E. North, Dana C. Crawford

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002138

Maps of Open Chromatin Guide the Functional Follow-Up of Genome-Wide Association Signals: Application to Hematological Traits

Dirk S. Paul, James P. Nisbet, Tsun-Po Yang, Stuart Meacham, Augusto Rendon, Katta Hautaviita, Jonna Tallila, Jacqui White, Marloes R. Tijssen, Suthesh Sivapalaratnam, Hanneke Basart, Mieke D. Trip, Consortium Cardiogenics, Consortium MuTHER, Berthold Göttgens, Nicole Soranzo, Willem H. Ouwehand, Panos Deloukas

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002139

A Two-Stage Meta-Analysis Identifies Several New Loci for Parkinson's Disease

International Parkinson's Disease Genomics Consortium (IPDGC), Wellcome Trust Case Control Consortium 2 (WTCCC2)

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002142

Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging-Related Transcriptional Networks

Tiara L. A. Kawahara, Nicole A. Rapicavoli, Angela R. Wu, Kun Qu, Stephen R. Quake, Howard Y. Chang

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002153

Role of the Single-Stranded DNA–Binding Protein SsbB in Pneumococcal Transformation: Maintenance of a Reservoir for Genetic Plasticity

Laetitia Attaiech, Audrey Olivier, Isabelle Mortier-Barrière, Anne-Lise Soulet, Chantal Granadel, Bernard Martin, Patrice Polard, Jean-Pierre Claverys

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002156

Identification of a Sudden Cardiac Death Susceptibility Locus at 2q24.2 through Genome-Wide Association in European Ancestry Individuals

Dan E. Arking, M. Juhani Junttila, Philippe Goyette, Adriana Huertas-Vazquez, Mark Eijgelsheim, Marieke T. Blom, Christopher Newton-Cheh, Kyndaron Reinier, Carmen Teodorescu, Audrey Uy-Evanado, Naima Carter-Monroe, Kari S. Kaikkonen, Marja-Leena Kortelainen, Gabrielle Boucher, Caroline Lagacé, Anna Moes, XiaoQing Zhao, Frank Kolodgie, Fernando Rivadeneira, Albert Hofman, Jacqueline C. M. Witteman, André G. Uitterlinden, Roos F. Marsman, Raha Pazoki, Abdennasser Bardai, Rudolph W. Koster, Abbas Dehghan, Shih-Jen Hwang, Pallav Bhatnagar, Wendy Post, Gina Hilton, Ronald J. Prineas, Man Li, Anna Köttgen, Georg Ehret, Eric Boerwinkle, Josef Coresh, W. H. Linda Kao, Bruce M. Psaty, Gordon F. Tomaselli, Nona Sotoodehnia, David S. Siscovick, Greg L. Burke, Eduardo Marbán, Peter M. Spooner, L. Adrienne Cupples, Jonathan Jui, Karen Gunson, Y. Antero Kesäniemi, Arthur A. M. Wilde, Jean-Claude Tardif, Christopher J. O'Donnell, Connie R. Bezzina, Renu Virmani, Bruno H. C. h. Stricker, Hanno L. Tan, Christine M. Albert, Aravinda Chakravarti, John D. Rioux, Heikki V. Huikuri, Sumeet S. Chugh

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002158

Transportin-SR Is Required for Proper Splicing of Resistance Genes and Plant Immunity

Shaohua Xu, Zhibin Zhang, Beibei Jing, Patrick Gannon, Jinmei Ding, Fang Xu, Xin Li, Yuelin Zhang

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002159

Telomere DNA Deficiency Is Associated with Development of Human Embryonic Aneuploidy

Nathan R. Treff, Jing Su, Deanne Taylor, Richard T. Scott Jr

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002161

Cryptic Transcription Mediates Repression of Subtelomeric Metal Homeostasis Genes

Isabelle Toesca, Camille R. Nery, Cesar F. Fernandez, Shakir Sayani, Guillaume F. Chanfreau

PLOS Genetics: published June 30, 2011 | https://doi.org/10.1371/journal.pgen.1002163

Interferon Regulatory Factor 8 Regulates Pathways for Antigen Presentation in Myeloid Cells and during Tuberculosis

Jean-François Marquis, Oxana Kapoustina, David Langlais, Rebecca Ruddy, Catherine Rosa Dufour, Bae-Hoon Kim, John D. MacMicking, Vincent Giguère, Philippe Gros

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002097

A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm

Ming Luo, Jennifer M. Taylor, Andrew Spriggs, Hongyu Zhang, Xianjun Wu, Scott Russell, Mohan Singh, Anna Koltunow

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002125

Increased Susceptibility to Cortical Spreading Depression in the Mouse Model of Familial Hemiplegic Migraine Type 2

Loredana Leo, Lisa Gherardini, Virginia Barone, Maurizio De Fusco, Daniela Pietrobon, Tommaso Pizzorusso, Giorgio Casari

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002129

Graded Nodal/Activin Signaling Titrates Conversion of Quantitative Phospho-Smad2 Levels into Qualitative Embryonic Stem Cell Fate Decisions

Kian Leong Lee, Sandy Keat Lim, Yuriy Lvovich Orlov, Le Yau Yit, Henry Yang, Lay Teng Ang, Lorenz Poellinger, Bing Lim

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002130

Differential Gene Expression and Epiregulation of Alpha Zein Gene Copies in Maize Haplotypes

Mihai Miclaus, Jian-Hong Xu, Joachim Messing

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002131

Web-Based Genome-Wide Association Study Identifies Two Novel Loci and a Substantial Genetic Component for Parkinson's Disease

Chuong B. Do, Joyce Y. Tung, Elizabeth Dorfman, Amy K. Kiefer, Emily M. Drabant, Uta Francke, Joanna L. Mountain, Samuel M. Goldman, Caroline M. Tanner, J. William Langston, Anne Wojcicki, Nicholas Eriksson

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002141

Genomic Convergence among ERRα, PROX1, and BMAL1 in the Control of Metabolic Clock Outputs

Catherine R. Dufour, Marie-Pier Levasseur, Nguyen Hoai Huong Pham, Lillian J. Eichner, Brian J. Wilson, Alexis Charest-Marcotte, David Duguay, Jean-François Poirier-Héon, Nicolas Cermakian, Vincent Giguère

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002143

Extracellular Matrix Dynamics in Hepatocarcinogenesis: a Comparative Proteomics Study of PDGFC Transgenic and Pten Null Mouse Models

Keane K. Y. Lai, Sufen Shang, Neha Lohia, Garrett C. Booth, Derek J. Masse, Nelson Fausto, Jean S. Campbell, Laura Beretta

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002147

Bacteriophage Crosstalk: Coordination of Prophage Induction by Trans-Acting Antirepressors

Sébastien Lemire, Nara Figueroa-Bossi, Lionello Bossi

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002149

A New Mutation Affecting FRQ-Less Rhythms in the Circadian System of Neurospora crassa

Sanshu Li, Kamyar Motavaze, Elizabeth Kafes, Sujiththa Suntharalingam, Patricia Lakin-Thomas

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002151

Unexpected Role for Helicobacter pylori DNA Polymerase I As a Source of Genetic Variability

María-Victoria García-Ortíz, Stéphanie Marsin, Mercedes E. Arana, Didier Gasparutto, Raphaël Guérois, Thomas A. Kunkel, J. Pablo Radicella

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002152

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells

Keith E. Szulwach, Xuekun Li, Yujing Li, Chun-Xiao Song, Ji Woong Han, SangSung Kim, Sandeep Namburi, Karen Hermetz, Julie J. Kim, M. Katharine Rudd, Young-Sup Yoon, Bing Ren, Chuan He, Peng Jin

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002154

Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites

Lars B. Scharff, Liam Childs, Dirk Walther, Ralph Bock

PLOS Genetics: published June 23, 2011 | https://doi.org/10.1371/journal.pgen.1002155

A Novel Approach to Selectively Target Neuronal Subpopulations Reveals Genetic Pathways That Regulate Tangential Migration in the Vertebrate Hindbrain

Karsten Benzing, Stefanie Flunkert, Andreas Schedl, Dieter Engelkamp

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002099

Trade-Off between Bile Resistance and Nutritional Competence Drives Escherichia coli Diversification in the Mouse Gut

Marianne De Paepe, Valérie Gaboriau-Routhiau, Dominique Rainteau, Sabine Rakotobe, François Taddei, Nadine Cerf-Bensussan

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002107

A Genome-Wide RNAi Screen for Factors Involved in Neuronal Specification in Caenorhabditis elegans

Richard J. Poole, Enkelejda Bashllari, Luisa Cochella, Eileen B. Flowers, Oliver Hobert

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002109

Trait Variation in Yeast Is Defined by Population History

Jonas Warringer, Enikö Zörgö, Francisco A. Cubillos, Amin Zia, Arne Gjuvsland, Jared T. Simpson, Annabelle Forsmark, Richard Durbin, Stig W. Omholt, Edward J. Louis, Gianni Liti, Alan Moses, Anders Blomberg

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002111

Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor

Sean Michael Carroll, Eric A. Ortlund, Joseph W. Thornton

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002117

Recurrent Chromosome 16p13.1 Duplications Are a Risk Factor for Aortic Dissections

Shao-Qing Kuang, Dong-Chuan Guo, Siddharth K. Prakash, Merry-Lynn N. McDonald, Ralph J. Johnson, Min Wang, Ellen S. Regalado, Ludivine Russell, Jiu-Mei Cao, Callie Kwartler, Kurt Fraivillig, Joseph S. Coselli, Hazim J. Safi, Anthony L. Estrera, Suzanne M. Leal, Scott A. LeMaire, John W. Belmont, Dianna M. Milewicz, GenTAC Investigators

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002118

How Chromatin Is Remodelled during DNA Repair of UV-Induced DNA Damage in Saccharomyces cerevisiae

Shirong Yu, Yumin Teng, Raymond Waters, Simon H. Reed

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002124

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm

Philip Wolff, Isabelle Weinhofer, Jonathan Seguin, Pawel Roszak, Christian Beisel, Mark T. A. Donoghue, Charles Spillane, Magnus Nordborg, Marc Rehmsmeier, Claudia Köhler

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002126

Parallel Adaptive Divergence among Geographically Diverse Human Populations

Jacob A. Tennessen, Joshua M. Akey

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002127

Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria

Frederic Bertels, Paul B. Rainey

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002132

SIRT1 Promotes N-Myc Oncogenesis through a Positive Feedback Loop Involving the Effects of MKP3 and ERK on N-Myc Protein Stability

Glenn M. Marshall, Pei Y. Liu, Samuele Gherardi, Christopher J. Scarlett, Antonio Bedalov, Ning Xu, Nuncio Iraci, Emanuele Valli, Dora Ling, Wayne Thomas, Margo van Bekkum, Eric Sekyere, Kacper Jankowski, Toby Trahair, Karen L. MacKenzie, Michelle Haber, Murray D. Norris, Andrew V. Biankin, Giovanni Perini, Tao Liu

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002135

Multiple Regulatory Mechanisms to Inhibit Untimely Initiation of DNA Replication Are Important for Stable Genome Maintenance

Seiji Tanaka, Hiroyuki Araki

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002136

Differential Effects of MYH9 and APOL1 Risk Variants on FRMD3 Association with Diabetic ESRD in African Americans

Barry I. Freedman, Carl D. Langefeld, Lingyi Lu, Jasmin Divers, Mary E. Comeau, Jeffrey B. Kopp, Cheryl A. Winkler, George W. Nelson, Randall C. Johnson, Nicholette D. Palmer, Pamela J. Hicks, Meredith A. Bostrom, Jessica N. Cooke, Caitrin W. McDonough, Donald W. Bowden

PLOS Genetics: published June 16, 2011 | https://doi.org/10.1371/journal.pgen.1002150

Epigenetic Patterns Maintained in Early Caenorhabditis elegans Embryos Can Be Established by Gene Activity in the Parental Germ Cells

Jackelyn K. Arico, David J. Katz, Johan van der Vlag, William G. Kelly

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1001391

A Large Gene Network in Immature Erythroid Cells Is Controlled by the Myeloid and B Cell Transcriptional Regulator PU.1

Sandeep N. Wontakal, Xingyi Guo, Britta Will, Minyi Shi, Debasish Raha, Milind C. Mahajan, Sherman Weissman, Michael Snyder, Ulrich Steidl, Deyou Zheng, Arthur I. Skoultchi

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1001392

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

Anatole Ghazalpour, Brian Bennett, Vladislav A. Petyuk, Luz Orozco, Raffi Hagopian, Imran N. Mungrue, Charles R. Farber, Janet Sinsheimer, Hyun M. Kang, Nicholas Furlotte, Christopher C. Park, Ping-Zi Wen, Heather Brewer, Karl Weitz, David G. Camp II, Calvin Pan, Roumyana Yordanova, Isaac Neuhaus, Charles Tilford, Nathan Siemers, Peter Gargalovic, Eleazar Eskin, Todd Kirchgessner, Desmond J. Smith, Richard D. Smith, Aldons J. Lusis

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1001393

Natural Allelic Variation Defines a Role for ATMYC1: Trichome Cell Fate Determination

V. Vaughan Symonds, Greg Hatlestad, Alan M. Lloyd

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002069

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

Stephen B. Goodwin, Sarrah Ben M'Barek, Braham Dhillon, Alexander H. J. Wittenberg, Charles F. Crane, James K. Hane, Andrew J. Foster, Theo A. J. Van der Lee, Jane Grimwood, Andrea Aerts, John Antoniw, Andy Bailey, Burt Bluhm, Judith Bowler, Jim Bristow, Ate van der Burgt, Blondy Canto-Canché, Alice C. L. Churchill, Laura Conde-Ferràez, Hans J. Cools, Pedro M. Coutinho, Michael Csukai, Paramvir Dehal, Pierre De Wit, Bruno Donzelli, Henri C. van de Geest, Roeland C. H. J. van Ham, Kim E. Hammond-Kosack, Bernard Henrissat, Andrzej Kilian, Adilson K. Kobayashi, Edda Koopmann, Yiannis Kourmpetis, Arnold Kuzniar, Erika Lindquist, Vincent Lombard, Chris Maliepaard, Natalia Martins, Rahim Mehrabi, Jan P. H. Nap, Alisa Ponomarenko, Jason J. Rudd, Asaf Salamov, Jeremy Schmutz, Henk J. Schouten, Harris Shapiro, Ioannis Stergiopoulos, Stefano F. F. Torriani, Hank Tu, Ronald P. de Vries, Cees Waalwijk, Sarah B. Ware, Ad Wiebenga, Lute-Harm Zwiers, Richard P. Oliver, Igor V. Grigoriev, Gert H. J. Kema

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002070

Exome Sequencing Identifies ZNF644 Mutations in High Myopia

Yi Shi, Yingrui Li, Dingding Zhang, Hao Zhang, Yuanfeng Li, Fang Lu, Xiaoqi Liu, Fei He, Bo Gong, Li Cai, Ruiqiang Li, Shihuang Liao, Shi Ma, He Lin, Jing Cheng, Hancheng Zheng, Ying Shan, Bin Chen, Jianbin Hu, Xin Jin, Peiquan Zhao, Yiye Chen, Yong Zhang, Ying Lin, Xi Li, Yingchuan Fan, Huanming Yang, Jun Wang, Zhenglin Yang

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002084

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

Ziwen He, Weiwei Zhai, Haijun Wen, Tian Tang, Yu Wang, Xuemei Lu, Anthony J. Greenberg, Richard R. Hudson, Chung-I Wu, Suhua Shi

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002100

Pathways of Distinction Analysis: A New Technique for Multi–SNP Analysis of GWAS Data

Rosemary Braun, Kenneth Buetow

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002101

Genetic Analysis of Genome-Scale Recombination Rate Evolution in House Mice

Beth L. Dumont, Bret A. Payseur

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002116

Specific SKN-1/Nrf Stress Responses to Perturbations in Translation Elongation and Proteasome Activity

Xuan Li, Olli Matilainen, Congyu Jin, Kira M. Glover-Cutter, Carina I. Holmberg, T. Keith Blackwell

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002119

Independent Chromatin Binding of ARGONAUTE4 and SPT5L/KTF1 Mediates Transcriptional Gene Silencing

M. Jordan Rowley, Maria I. Avrutsky, Christopher J. Sifuentes, Ligia Pereira, Andrzej T. Wierzbicki

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002120

Meiosis-Specific Loading of the Centromere-Specific Histone CENH3 in Arabidopsis thaliana

Maruthachalam Ravi, Fukashi Shibata, Joseph S. Ramahi, Kiyotaka Nagaki, Changbin Chen, Minoru Murata, Simon W. L. Chan

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002121

Cooperative and Antagonistic Contributions of Two Heterochromatin Proteins to Transcriptional Regulation of the Drosophila Sex Determination Decision

Hui Li, Janel Rodriguez, Youngdong Yoo, Momin Mohammed Shareef, RamaKrishna Badugu, Jamila I. Horabin, Rebecca Kellum

PLOS Genetics: published June 9, 2011 | https://doi.org/10.1371/journal.pgen.1002122

A New Isoform of the Histone Demethylase JMJD2A/KDM4A Is Required for Skeletal Muscle Differentiation

Laure Verrier, Fabrice Escaffit, Catherine Chailleux, Didier Trouche, Marie Vandromme

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1001390

Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus

Darin R. Rokyta, Paul Joyce, S. Brian Caudle, Craig Miller, Craig J. Beisel, Holly A. Wichman

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002075

DNA Ligase III Promotes Alternative Nonhomologous End-Joining during Chromosomal Translocation Formation

Deniz Simsek, Erika Brunet, Sunnie Yan-Wai Wong, Sachin Katyal, Yankun Gao, Peter J. McKinnon, Jacqueline Lou, Lei Zhang, James Li, Edward J. Rebar, Philip D. Gregory, Michael C. Holmes, Maria Jasin

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002080

Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells

Florian Lienert, Fabio Mohn, Vijay K. Tiwari, Tuncay Baubec, Tim C. Roloff, Dimos Gaidatzis, Michael B. Stadler, Dirk Schübeler

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002090

Mammalian BTBD12 (SLX4) Protects against Genomic Instability during Mammalian Spermatogenesis

J. Kim Holloway, Swapna Mohan, Gabriel Balmus, Xianfei Sun, Andrew Modzelewski, Peter L. Borst, Raimundo Freire, Robert S. Weiss, Paula E. Cohen

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002094

Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element

Antoine Barrière, Kacy L. Gordon, Ilya Ruvinsky

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002095

FGF Signaling Regulates the Number of Posterior Taste Papillae by Controlling Progenitor Field Size

Camille I. Petersen, Andrew H. Jheon, Pasha Mostowfi, Cyril Charles, Saunders Ching, Shoba Thirumangalathu, Linda A. Barlow, Ophir D. Klein

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002098

Nuclear Accumulation of Stress Response mRNAs Contributes to the Neurodegeneration Caused by Fragile X Premutation rCGG Repeats

Abrar Qurashi, Wendi Li, Jian-Ying Zhou, Junmin Peng, Peng Jin

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002102

Chk2 and p53 Are Haploinsufficient with Dependent and Independent Functions to Eliminate Cells after Telomere Loss

Rebeccah L. Kurzhals, Simon W. A. Titen, Heng B. Xie, Kent G. Golic

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002103

Pathogenic Mechanism of the FIG4 Mutation Responsible for Charcot-Marie-Tooth Disease CMT4J

Guy M. Lenk, Cole J. Ferguson, Clement Y. Chow, Natsuko Jin, Julie M. Jones, Adrienne E. Grant, Sergey N. Zolov, Jesse J. Winters, Roman J. Giger, James J. Dowling, Lois S. Weisman, Miriam H. Meisler

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002104

Multiple Common Susceptibility Variants near BMP Pathway Loci GREM1, BMP4, and BMP2 Explain Part of the Missing Heritability of Colorectal Cancer

Ian P. M. Tomlinson, Luis G. Carvajal-Carmona, Sara E. Dobbins, Albert Tenesa, Angela M. Jones, Kimberley Howarth, Claire Palles, Peter Broderick, Emma E. M. Jaeger, Susan Farrington, Annabelle Lewis, James G. D. Prendergast, Alan M. Pittman, Evropi Theodoratou, Bianca Olver, Marion Walker, Steven Penegar, Ella Barclay, Nicola Whiffin, Lynn Martin, Stephane Ballereau, Amy Lloyd, Maggie Gorman, Steven Lubbe, The COGENT Consortium, The CORGI Collaborators, The EPICOLON Consortium, Bryan Howie, Jonathan Marchini, Clara Ruiz-Ponte, Ceres Fernandez-Rozadilla, Antoni Castells, Angel Carracedo, Sergi Castellvi-Bel, David Duggan, David Conti, Jean-Baptiste Cazier, Harry Campbell, Oliver Sieber, Lara Lipton, Peter Gibbs, Nicholas G. Martin, Grant W. Montgomery, Joanne Young, Paul N. Baird, Steven Gallinger, Polly Newcomb, John Hopper, Mark A. Jenkins, Lauri A. Aaltonen, David J. Kerr, Jeremy Cheadle, Paul Pharoah, Graham Casey, Richard S. Houlston, Malcolm G. Dunlop

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002105

CorE from Myxococcus xanthus Is a Copper-Dependent RNA Polymerase Sigma Factor

Nuria Gómez-Santos, Juana Pérez, María Celestina Sánchez-Sutil, Aurelio Moraleda-Muñoz, José Muñoz-Dorado

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002106

Genome-Wide Analysis Reveals PADI4 Cooperates with Elk-1 to Activate c-Fos Expression in Breast Cancer Cells

Xuesen Zhang, Matthew J. Gamble, Sonja Stadler, Brian D. Cherrington, Corey P. Causey, Paul R. Thompson, Mark S. Roberson, W. Lee Kraus, Scott A. Coonrod

PLOS Genetics: published June 2, 2011 | https://doi.org/10.1371/journal.pgen.1002112

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