# wombat urls ß PLOS Genetics: A Peer-Reviewed Open-Access Journal
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Table of Contents: November 2011

COVER

The ER in abstraction.

Image Credit: Stephanie Kinkel (Massachusetts Institute of Technology)
Issue Image

The endoplasmic reticulum is depicted crowded with proteins at varied stages in synthesis and folding. The study of Richardson et al. supports the concept that the Unfolded Protein Response is activated and maintains ER homeostasis during physiological conditions such as larval development and innate immunity.

Perspectives

De Novo Origins of Human Genes

Daniele Guerzoni, Aoife McLysaght

Research Articles

Role of Pirh2 in Mediating the Regulation of p53 and c-Myc

Anne Hakem, Miyuki Bohgaki, Bénédicte Lemmers, Elisabeth Tai, Leonardo Salmena, Elzbieta Matysiak-Zablocki, Yong-Sam Jung, Jana Karaskova, Lilia Kaustov, Shili Duan, Jason Madore, Paul Boutros, Yi Sheng, Marta Chesi, P. Leif Bergsagel, Bayardo Perez-Ordonez, Anne-Marie Mes-Masson, Linda Penn, Jeremy Squire, Xinbin Chen, Igor Jurisica, Cheryl Arrowsmith, Otto Sanchez, Samuel Benchimol, Razqallah Hakem

The SUN Protein Mps3 Is Required for Spindle Pole Body Insertion into the Nuclear Membrane and Nuclear Envelope Homeostasis

Jennifer M. Friederichs, Suman Ghosh, Christine J. Smoyer, Scott McCroskey, Brandon D. Miller, Kyle J. Weaver, Kym M. Delventhal, Jay Unruh, Brian D. Slaughter, Sue L. Jaspersen

PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer

Luca Magnani, Elizabeth B. Ballantyne, Xiaoyang Zhang, Mathieu Lupien

The NF1 Gene Contains Hotspots for L1 Endonuclease-Dependent De Novo Insertion

Katharina Wimmer, Tom Callens, Annekatrin Wernstedt, Ludwine Messiaen

Heritable Epigenetic Variation among Maize Inbreds

Steve R. Eichten, Ruth A. Swanson-Wagner, James C. Schnable, Amanda J. Waters, Peter J. Hermanson, Sanzhen Liu, Cheng-Ting Yeh, Yi Jia, Karla Gendler, Michael Freeling, Patrick S. Schnable, Matthew W. Vaughn, Nathan M. Springer

Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

Mohan Babu, J. Javier Díaz-Mejía, James Vlasblom, Alla Gagarinova, Sadhna Phanse, Chris Graham, Fouad Yousif, Huiming Ding, Xuejian Xiong, Anaies Nazarians-Armavil, Md Alamgir, Mehrab Ali, Oxana Pogoutse, Asaf Pe'er, Roland Arnold, Magali Michaut, John Parkinson, Ashkan Golshani, Chris Whitfield, Shoshana J. Wodak, Gabriel Moreno-Hagelsieb, Jack F. Greenblatt, Andrew Emili

Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize

Patrick J. Brown, Narasimham Upadyayula, Gregory S. Mahone, Feng Tian, Peter J. Bradbury, Sean Myles, James B. Holland, Sherry Flint-Garcia, Michael D. McMullen, Edward S. Buckler, Torbert R. Rocheford

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

Adam Deutschbauer, Morgan N. Price, Kelly M. Wetmore, Wenjun Shao, Jason K. Baumohl, Zhuchen Xu, Michelle Nguyen, Raquel Tamse, Ronald W. Davis, Adam P. Arkin

Relative Burden of Large CNVs on a Range of Neurodevelopmental Phenotypes

Santhosh Girirajan, Zoran Brkanac, Bradley P. Coe, Carl Baker, Laura Vives, Tiffany H. Vu, Neil Shafer, Raphael Bernier, Giovanni B. Ferrero, Margherita Silengo, Stephen T. Warren, Carlos S. Moreno, Marco Fichera, Corrado Romano, Wendy H. Raskind, Evan E. Eichler

Multiple Means to the Same End: The Genetic Basis of Acquired Stress Resistance in Yeast

David B. Berry, Qiaoning Guan, James Hose, Suraiya Haroon, Marinella Gebbia, Lawrence E. Heisler, Corey Nislow, Guri Giaever, Audrey P. Gasch

Serratia symbiotica from the Aphid Cinara cedri: A Missing Link from Facultative to Obligate Insect Endosymbiont

Araceli Lamelas, María José Gosalbes, Alejandro Manzano-Marín, Juli Peretó, Andrés Moya, Amparo Latorre

Caenorhabditis elegans Cyclin D/CDK4 and Cyclin E/CDK2 Induce Distinct Cell Cycle Re-Entry Programs in Differentiated Muscle Cells

Jerome Korzelius, Inge The, Suzan Ruijtenberg, Martine B. W. Prinsen, Vincent Portegijs, Teije C. Middelkoop, Marian J. Groot Koerkamp, Frank C. P. Holstege, Mike Boxem, Sander van den Heuvel

Capture of MicroRNA–Bound mRNAs Identifies the Tumor Suppressor miR-34a as a Regulator of Growth Factor Signaling

Ashish Lal, Marshall P. Thomas, Gabriel Altschuler, Francisco Navarro, Elizabeth O'Day, Xiao Ling Li, Carla Concepcion, Yoon-Chi Han, Jerome Thiery, Danielle K. Rajani, Aaron Deutsch, Oliver Hofmann, Andrea Ventura, Winston Hide, Judy Lieberman

Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness

Michael Z. Ludwig, Manu, Ralf Kittler, Kevin P. White, Martin Kreitman

The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

Sylvia E. J. Fischer, Taiowa A. Montgomery, Chi Zhang, Noah Fahlgren, Peter C. Breen, Alexia Hwang, Christopher M. Sullivan, James C. Carrington, Gary Ruvkun

FOXO Regulates Organ-Specific Phenotypic Plasticity In Drosophila

Hui Yuan Tang, Martha S. B. Smith-Caldas, Michael V. Driscoll, Samy Salhadar, Alexander W. Shingleton

De Novo Origin of Human Protein-Coding Genes

Dong-Dong Wu, David M. Irwin, Ya-Ping Zhang

Drosophila Duplication Hotspots Are Associated with Late-Replicating Regions of the Genome

Margarida Cardoso-Moreira, J. J. Emerson, Andrew G. Clark, Manyuan Long

Over-Expression of DSCAM and COL6A2 Cooperatively Generates Congenital Heart Defects

Tamar R. Grossman, Amir Gamliel, Robert J. Wessells, Ouarda Taghli-Lamallem, Kristen Jepsen, Karen Ocorr, Julie R. Korenberg, Kirk L. Peterson, Michael G. Rosenfeld, Rolf Bodmer, Ethan Bier

Foxn1 Regulates Lineage Progression in Cortical and Medullary Thymic Epithelial Cells But Is Dispensable for Medullary Sublineage Divergence

Craig S. Nowell, Nicholas Bredenkamp, Stéphanie Tetélin, Xin Jin, Christin Tischner, Harsh Vaidya, Julie M. Sheridan, Frances Hogg Stenhouse, Raphaela Heussen, Andrew J. H. Smith, C. Clare Blackburn

Attenuation of the Sensing Capabilities of PhoQ in Transition to Obligate Insect–Bacterial Association

Mauricio Henriques Pontes, Kari Lyn Smith, Linda De Vooght, Jan Van Den Abbeele, Colin Dale

Genome-Wide Crossover Distribution in Arabidopsis thaliana Meiosis Reveals Sex-Specific Patterns along Chromosomes

Laurène Giraut, Matthieu Falque, Jan Drouaud, Lucie Pereira, Olivier C. Martin, Christine Mézard

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

Matteo Fumagalli, Manuela Sironi, Uberto Pozzoli, Anna Ferrer-Admettla, Linda Pattini, Rasmus Nielsen

SOX9 Governs Differentiation Stage-Specific Gene Expression in Growth Plate Chondrocytes via Direct Concomitant Transactivation and Repression

Victor Y. L. Leung, Bo Gao, Keith K. H. Leung, Ian G. Melhado, Sarah L. Wynn, Tiffany Y. K. Au, Nelson W. F. Dung, James Y. B. Lau, Angel C. Y. Mak, Danny Chan, Kathryn S. E. Cheah

A Novel Protein LZTFL1 Regulates Ciliary Trafficking of the BBSome and Smoothened

Seongjin Seo, Qihong Zhang, Kevin Bugge, David K. Breslow, Charles C. Searby, Maxence V. Nachury, Val C. Sheffield

Activation of Bmp2-Smad1 Signal and Its Regulation by Coordinated Alteration of H3K27 Trimethylation in Ras-Induced Senescence

Atsushi Kaneda, Takanori Fujita, Motonobu Anai, Shogo Yamamoto, Genta Nagae, Masato Morikawa, Shingo Tsuji, Masanobu Oshima, Kohei Miyazono, Hiroyuki Aburatani