June 2015

Confocal laser scanning microscopy image of a nodule section illustrating the internal infection pattern of the endophyte Rhizobium mesosinicum, strain KAW12 (red) and of the incompatible symbiont Mesorhizobium loti, strain exoU (green). Zgadzaj et al.

Image Credit: Rafal Zgadzaj

Perspectives

Minor Cause—Major Effect: A Novel Mode of Control of Bistable Gene Expression

Jan Kampf, Jörg Stülke

PLOS Genetics: published June 25, 2015 | https://doi.org/10.1371/journal.pgen.1005229

Orphan Genes Find a Home: Interspecific Competition and Gene Network Evolution

Karley K. Mahalak, Helen M. Chamberlin

PLOS Genetics: published June 18, 2015 | https://doi.org/10.1371/journal.pgen.1005254

Connecting Circadian Genes to Neurodegenerative Pathways in Fruit Flies

Patrick Emery

PLOS Genetics: published June 11, 2015 | https://doi.org/10.1371/journal.pgen.1005266

Research Articles

Independent Neuronal Origin of Seizures and Behavioral Comorbidities in an Animal Model of a Severe Childhood Genetic Epileptic Encephalopathy

Samuel K. Asinof, Stacey J. Sukoff Rizzo, Alexandra R. Buckley, Barbara J. Beyer, Verity A. Letts, Wayne N. Frankel, Rebecca M. Boumil

PLOS Genetics: published June 30, 2015 | https://doi.org/10.1371/journal.pgen.1005347

Drosophila Lipophorin Receptors Recruit the Lipoprotein LTP to the Plasma Membrane to Mediate Lipid Uptake

Míriam Rodríguez-Vázquez, David Vaquero, Esmeralda Parra-Peralbo, John E. Mejía-Morales, Joaquim Culi

PLOS Genetics: published June 29, 2015 | https://doi.org/10.1371/journal.pgen.1005356

Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity within and between Drosophila Species

Winslow C. Johnson, Alison J. Ordway, Masayoshi Watada, Jonathan N. Pruitt, Thomas M. Williams, Mark Rebeiz

PLOS Genetics: published June 26, 2015 | https://doi.org/10.1371/journal.pgen.1005279

Motor and Sensory Deficits in the teetering Mice Result from Mutation of the ESCRT Component HGS

Jennifer A. Watson, Bula J. Bhattacharyya, Jada H. Vaden, Julie A. Wilson, Mert Icyuz, Alan D. Howard, Edward Phillips, Tara M. DeSilva, Gene P. Siegal, Andrew J. Bean, Gwendalyn D. King, Scott E. Phillips, Richard J. Miller, Scott M. Wilson

PLOS Genetics: published June 26, 2015 | https://doi.org/10.1371/journal.pgen.1005290

Orthodenticle Is Required for the Expression of Principal Recognition Molecules That Control Axon Targeting in the Drosophila Retina

Chiara Mencarelli, Franck Pichaud

PLOS Genetics: published June 26, 2015 | https://doi.org/10.1371/journal.pgen.1005303

Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes

Janna L. Fierst, John H. Willis, Cristel G. Thomas, Wei Wang, Rose M. Reynolds, Timothy E. Ahearne, Asher D. Cutter, Patrick C. Phillips

PLOS Genetics: published June 26, 2015 | https://doi.org/10.1371/journal.pgen.1005323

Context-Dependent Functional Divergence of the Notch Ligands DLL1 and DLL4 In Vivo

Kristina Preuße, Lena Tveriakhina, Karin Schuster-Gossler, Cláudia Gaspar, Alexandra Isabel Rosa, Domingos Henrique, Achim Gossler, Michael Stauber

PLOS Genetics: published June 26, 2015 | https://doi.org/10.1371/journal.pgen.1005328

Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila

Qi Zhou, Doris Bachtrog

PLOS Genetics: published June 26, 2015 | https://doi.org/10.1371/journal.pgen.1005331

Separable Crossover-Promoting and Crossover-Constraining Aspects of Zip1 Activity during Budding Yeast Meiosis

Karen Voelkel-Meiman, Cassandra Johnston, Yashna Thappeta, Vijayalakshmi V. Subramanian, Andreas Hochwagen, Amy J. MacQueen

PLOS Genetics: published June 26, 2015 | https://doi.org/10.1371/journal.pgen.1005335

Abnormal Activation of BMP Signaling Causes Myopathy in Fbn2 Null Mice

Gerhard Sengle, Valerie Carlberg, Sara F. Tufa, Noe L. Charbonneau, Silvia Smaldone, Eric J. Carlson, Francesco Ramirez, Douglas R. Keene, Lynn Y. Sakai

PLOS Genetics: published June 26, 2015 | https://doi.org/10.1371/journal.pgen.1005340

Silencing of DNase Colicin E8 Gene Expression by a Complex Nucleoprotein Assembly Ensures Timely Colicin Induction

Simona Kamenšek, Douglas F. Browning, Zdravko Podlesek, Stephen J. W. Busby, Darja Žgur-Bertok, Matej Butala

PLOS Genetics: published June 26, 2015 | https://doi.org/10.1371/journal.pgen.1005354

A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence

Pamela Gamba, Martijs J. Jonker, Leendert W. Hamoen

PLOS Genetics: published June 25, 2015 | https://doi.org/10.1371/journal.pgen.1005047

AKTIP/Ft1, a New Shelterin-Interacting Factor Required for Telomere Maintenance

Romina Burla, Mariateresa Carcuro, Grazia D. Raffa, Alessandra Galati, Domenico Raimondo, Angela Rizzo, Mattia La Torre, Emanuela Micheli, Laura Ciapponi, Giovanni Cenci, Enrico Cundari, Antonio Musio, Annamaria Biroccio, Stefano Cacchione, Maurizio Gatti, Isabella Saggio

PLOS Genetics: published June 25, 2015 | https://doi.org/10.1371/journal.pgen.1005167

The Analysis of Pendolino (peo) Mutants Reveals Differences in the Fusigenic Potential among Drosophila Telomeres

Giovanni Cenci, Laura Ciapponi, Marta Marzullo, Grazia D. Raffa, Patrizia Morciano, Domenico Raimondo, Romina Burla, Isabella Saggio, Maurizio Gatti

PLOS Genetics: published June 25, 2015 | https://doi.org/10.1371/journal.pgen.1005260

Epigenetic Aging Signatures Are Coherently Modified in Cancer

Qiong Lin, Wolfgang Wagner

PLOS Genetics: published June 25, 2015 | https://doi.org/10.1371/journal.pgen.1005334

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding

Xin Xie, Michael J. T. Stubbington, Jesper K. Nissen, Kristian G. Andersen, Daniel Hebenstreit, Sarah A. Teichmann, Alexander G. Betz

PLOS Genetics: published June 24, 2015 | https://doi.org/10.1371/journal.pgen.1005251

Dissection of a Complex Disease Susceptibility Region Using a Bayesian Stochastic Search Approach to Fine Mapping

Chris Wallace, Antony J Cutler, Nikolas Pontikos, Marcin L Pekalski, Oliver S Burren, Jason D Cooper, Arcadio Rubio García, Ricardo C Ferreira, Hui Guo, Neil M Walker, Deborah J Smyth, Stephen S Rich, Suna Onengut-Gumuscu, Stephen J Sawcer, Maria Ban, Sylvia Richardson, John A Todd, Linda S Wicker

PLOS Genetics: published June 24, 2015 | https://doi.org/10.1371/journal.pgen.1005272

Translational Upregulation of an Individual p21^Cip1 Transcript Variant by GCN2 Regulates Cell Proliferation and Survival under Nutrient Stress

Stacey L. Lehman, George J. Cerniglia, Gregg J. Johannes, Jiangbin Ye, Sandra Ryeom, Constantinos Koumenis

PLOS Genetics: published June 23, 2015 | https://doi.org/10.1371/journal.pgen.1005212

Germline ETV6 Mutations Confer Susceptibility to Acute Lymphoblastic Leukemia and Thrombocytopenia

Sabine Topka, Joseph Vijai, Michael F. Walsh, Lauren Jacobs, Ann Maria, Danylo Villano, Pragna Gaddam, Gang Wu, Rose B. McGee, Emily Quinn, Hiroto Inaba, Christine Hartford, Ching-hon Pui, Alberto Pappo, Michael Edmonson, Michael Y. Zhang, Polina Stepensky, Peter Steinherz, Kasmintan Schrader, Anne Lincoln, James Bussel, Steve M. Lipkin, Yehuda Goldgur, Mira Harit, Zsofia K. Stadler, Charles Mullighan, Michael Weintraub, Akiko Shimamura, Jinghui Zhang, James R. Downing, Kim E. Nichols, Kenneth Offit

PLOS Genetics: published June 23, 2015 | https://doi.org/10.1371/journal.pgen.1005262

The Eukaryotic-Like Ser/Thr Kinase PrkC Regulates the Essential WalRK Two-Component System in Bacillus subtilis

Elizabeth A. Libby, Lindsie A. Goss, Jonathan Dworkin

PLOS Genetics: published June 23, 2015 | https://doi.org/10.1371/journal.pgen.1005275

The Yeast GSK-3 Homologue Mck1 Is a Key Controller of Quiescence Entry and Chronological Lifespan

Zhenzhen Quan, Lu Cao, Yingzhi Tang, Yanchun Yan, Stephen G. Oliver, Nianshu Zhang

PLOS Genetics: published June 23, 2015 | https://doi.org/10.1371/journal.pgen.1005282

Regulation of Insulin Receptor Trafficking by Bardet Biedl Syndrome Proteins

Rachel D. Starks, Andreas M. Beyer, Deng Fu Guo, Lauren Boland, Qihong Zhang, Val C. Sheffield, Kamal Rahmouni

PLOS Genetics: published June 23, 2015 | https://doi.org/10.1371/journal.pgen.1005311

FGFR3 Deficiency Causes Multiple Chondroma-like Lesions by Upregulating Hedgehog Signaling

Siru Zhou, Yangli Xie, Junzhou Tang, Junlan Huang, Qizhao Huang, Wei Xu, Zuqiang Wang, Fengtao Luo, Quan Wang, Hangang Chen, Xiaolan Du, Yue Shen, Di Chen, Lin Chen

PLOS Genetics: published June 19, 2015 | https://doi.org/10.1371/journal.pgen.1005214

DNA Damage Regulates Translation through β-TRCP Targeting of CReP

Theresa B. Loveless, Benjamin R. Topacio, Ajay A. Vashisht, Shastyn Galaang, Katie M. Ulrich, Brian D. Young, James A. Wohlschlegel, David P. Toczyski

PLOS Genetics: published June 19, 2015 | https://doi.org/10.1371/journal.pgen.1005292

MreB-Dependent Inhibition of Cell Elongation during the Escape from Competence in Bacillus subtilis

Nicolas Mirouze, Cécile Ferret, Zhizhong Yao, Arnaud Chastanet, Rut Carballido-López

PLOS Genetics: published June 19, 2015 | https://doi.org/10.1371/journal.pgen.1005299

Transfer RNAs Mediate the Rapid Adaptation of Escherichia coli to Oxidative Stress

Jiayong Zhong, Chuanle Xiao, Wei Gu, Gaofei Du, Xuesong Sun, Qing-Yu He, Gong Zhang

PLOS Genetics: published June 19, 2015 | https://doi.org/10.1371/journal.pgen.1005302

The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation

Melanie G. Mayer, Christian Rödelsperger, Hanh Witte, Metta Riebesell, Ralf J. Sommer

PLOS Genetics: published June 18, 2015 | https://doi.org/10.1371/journal.pgen.1005146

The Human Blood Metabolome-Transcriptome Interface

Jörg Bartel, Jan Krumsiek, Katharina Schramm, Jerzy Adamski, Christian Gieger, Christian Herder, Maren Carstensen, Annette Peters, Wolfgang Rathmann, Michael Roden, Konstantin Strauch, Karsten Suhre, Gabi Kastenmüller, Holger Prokisch, Fabian J. Theis

PLOS Genetics: published June 18, 2015 | https://doi.org/10.1371/journal.pgen.1005274

Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm

Carolin A. Rebernig, Clément Lafon-Placette, Marcelinus R. Hatorangan, Tanja Slotte, Claudia Köhler

PLOS Genetics: published June 18, 2015 | https://doi.org/10.1371/journal.pgen.1005295

The Causative Gene in Chanarian Dorfman Syndrome Regulates Lipid Droplet Homeostasis in C. elegans

Meng Xie, Richard Roy

PLOS Genetics: published June 17, 2015 | https://doi.org/10.1371/journal.pgen.1005284

A Transposable Element within the Non-canonical Telomerase RNA of Arabidopsis thaliana Modulates Telomerase in Response to DNA Damage

Hengyi Xu, Andrew D. L. Nelson, Dorothy E. Shippen

PLOS Genetics: published June 15, 2015 | https://doi.org/10.1371/journal.pgen.1005281

Npvf: Hypothalamic Biomarker of Ambient Temperature Independent of Nutritional Status

Julia Jaroslawska, Agnieszka Chabowska-Kita, Monika M. Kaczmarek, Leslie P. Kozak

PLOS Genetics: published June 12, 2015 | https://doi.org/10.1371/journal.pgen.1005287

The B. subtilis Accessory Helicase PcrA Facilitates DNA Replication through Transcription Units

Christopher N. Merrikh, Bonita J. Brewer, Houra Merrikh

PLOS Genetics: published June 12, 2015 | https://doi.org/10.1371/journal.pgen.1005289

Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth

Debora Gasperini, Aurore Chételat, Ivan F. Acosta, Jonas Goossens, Laurens Pauwels, Alain Goossens, René Dreos, Esteban Alfonso, Edward E. Farmer

PLOS Genetics: published June 12, 2015 | https://doi.org/10.1371/journal.pgen.1005300

Necrotic Cells Actively Attract Phagocytes through the Collaborative Action of Two Distinct PS-Exposure Mechanisms

Zao Li, Victor Venegas, Yuji Nagaoka, Eri Morino, Prashant Raghavan, Anjon Audhya, Yoshinobu Nakanishi, Zheng Zhou

PLOS Genetics: published June 10, 2015 | https://doi.org/10.1371/journal.pgen.1005285

Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner

Nicolas Carraro, Dominique Poulin, Vincent Burrus

PLOS Genetics: published June 10, 2015 | https://doi.org/10.1371/journal.pgen.1005298

Multiple Changes of Gene Expression and Function Reveal Genomic and Phenotypic Complexity in SLE-like Disease

Maria Wilbe, Sergey V. Kozyrev, Fabiana H. G. Farias, Hanna D. Bremer, Anna Hedlund, Gerli R. Pielberg, Eija H. Seppälä, Ulla Gustafson, Hannes Lohi, Örjan Carlborg, Göran Andersson, Helene Hansson-Hamlin, Kerstin Lindblad-Toh

PLOS Genetics: published June 9, 2015 | https://doi.org/10.1371/journal.pgen.1005248

In Vivo Senescence in the Sbds-Deficient Murine Pancreas: Cell-Type Specific Consequences of Translation Insufficiency

Marina E. Tourlakis, Siyi Zhang, Heather L. Ball, Rikesh Gandhi, Hongrui Liu, Jian Zhong, Julie S. Yuan, Cynthia J. Guidos, Peter R. Durie, Johanna M. Rommens

PLOS Genetics: published June 9, 2015 | https://doi.org/10.1371/journal.pgen.1005288

A Common Cancer Risk-Associated Allele in the hTERT Locus Encodes a Dominant Negative Inhibitor of Telomerase

Anagha Killedar, Michael D. Stutz, Alexander P. Sobinoff, Christopher G. Tomlinson, Tracy M. Bryan, Jonathan Beesley, Georgia Chenevix-Trench, Roger R. Reddel, Hilda A. Pickett

PLOS Genetics: published June 8, 2015 | https://doi.org/10.1371/journal.pgen.1005286

Exome Sequencing of Phenotypic Extremes Identifies CAV2 and TMC6 as Interacting Modifiers of Chronic Pseudomonas aeruginosa Infection in Cystic Fibrosis

Mary J. Emond, Tin Louie, Julia Emerson, Jessica X. Chong, Rasika A. Mathias, Michael R. Knowles, Mark J. Rieder, Holly K. Tabor, Debbie A. Nickerson, Kathleen C. Barnes, NHLBI GO Exome Sequencing Project, Lung GO, Ronald L. Gibson, Michael J. Bamshad

PLOS Genetics: published June 5, 2015 | https://doi.org/10.1371/journal.pgen.1005273

The DnaA Protein Is Not the Limiting Factor for Initiation of Replication in Escherichia coli

Ingvild Flåtten, Solveig Fossum-Raunehaug, Riikka Taipale, Silje Martinsen, Kirsten Skarstad

PLOS Genetics: published June 5, 2015 | https://doi.org/10.1371/journal.pgen.1005276

Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination

Taejin Kim, Sindhu Chitteni-Pattu, Benjamin L. Cox, Elizabeth A. Wood, Steven J. Sandler, Michael M. Cox

PLOS Genetics: published June 5, 2015 | https://doi.org/10.1371/journal.pgen.1005278

Multiple In Vivo Biological Processes Are Mediated by Functionally Redundant Activities of Drosophila mir-279 and mir-996

Kailiang Sun, David Jee, Luis F. de Navas, Hong Duan, Eric C. Lai

PLOS Genetics: published June 4, 2015 | https://doi.org/10.1371/journal.pgen.1005245

The Role of piRNA-Mediated Epigenetic Silencing in the Population Dynamics of Transposable Elements in Drosophila melanogaster

Yuh Chwen G. Lee

PLOS Genetics: published June 4, 2015 | https://doi.org/10.1371/journal.pgen.1005269

Leveraging Identity-by-Descent for Accurate Genotype Inference in Family Sequencing Data

Bingshan Li, Qiang Wei, Xiaowei Zhan, Xue Zhong, Wei Chen, Chun Li, Jonathan Haines

PLOS Genetics: published June 4, 2015 | https://doi.org/10.1371/journal.pgen.1005271

A Legume Genetic Framework Controls Infection of Nodules by Symbiotic and Endophytic Bacteria

Rafal Zgadzaj, Euan K. James, Simon Kelly, Yasuyuki Kawaharada, Nadieh de Jonge, Dorthe B. Jensen, Lene H. Madsen, Simona Radutoiu

PLOS Genetics: published June 4, 2015 | https://doi.org/10.1371/journal.pgen.1005280

Temporal Expression Profiling Identifies Pathways Mediating Effect of Causal Variant on Phenotype

Saumya Gupta, Aparna Radhakrishnan, Pandu Raharja-Liu, Gen Lin, Lars M. Steinmetz, Julien Gagneur, Himanshu Sinha

PLOS Genetics: published June 3, 2015 | https://doi.org/10.1371/journal.pgen.1005195

Altered Levels of Mitochondrial DNA Are Associated with Female Age, Aneuploidy, and Provide an Independent Measure of Embryonic Implantation Potential

Elpida Fragouli, Katharina Spath, Samer Alfarawati, Fiona Kaper, Andrew Craig, Claude-Edouard Michel, Felix Kokocinski, Jacques Cohen, Santiago Munne, Dagan Wells

PLOS Genetics: published June 3, 2015 | https://doi.org/10.1371/journal.pgen.1005241

Functional Assessment of Disease-Associated Regulatory Variants In Vivo Using a Versatile Dual Colour Transgenesis Strategy in Zebrafish

Shipra Bhatia, Christopher T. Gordon, Robert G. Foster, Lucie Melin, Véronique Abadie, Geneviève Baujat, Marie-Paule Vazquez, Jeanne Amiel, Stanislas Lyonnet, Veronica van Heyningen, Dirk A. Kleinjan

PLOS Genetics: published June 1, 2015 | https://doi.org/10.1371/journal.pgen.1005193

9-cis-13,14-Dihydroretinoic Acid Is an Endogenous Retinoid Acting as RXR Ligand in Mice

Ralph Rühl, Agnieszka Krzyżosiak, Anna Niewiadomska-Cimicka, Natacha Rochel, Lajos Szeles, Belén Vaz, Marta Wietrzych-Schindler, Susana Álvarez, Monika Szklenar, Laszlo Nagy, Angel R. de Lera, Wojciech Krężel

PLOS Genetics: published June 1, 2015 | https://doi.org/10.1371/journal.pgen.1005213

Canine Spontaneous Head and Neck Squamous Cell Carcinomas Represent Their Human Counterparts at the Molecular Level

Deli Liu, Huan Xiong, Angela E. Ellis, Nicole C. Northrup, Kevin K. Dobbin, Dong M. Shin, Shaying Zhao

PLOS Genetics: published June 1, 2015 | https://doi.org/10.1371/journal.pgen.1005277

Expression of Concern

Expression of Concern: RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells

The PLOS Genetics Editors

PLOS Genetics: published June 29, 2015 | https://doi.org/10.1371/journal.pgen.1005377

Formal Comments

Response to the Formal Letter of Z. Chrzanowska-Lightowlers and R. N. Lightowlers Regarding Our Article “Ribosome Rescue and Translation Termination at Non-Standard Stop Codons by ICT1 in Mammalian Mitochondria”

Nono Takeuchi, Knud H. Nierhaus

PLOS Genetics: published June 18, 2015 | https://doi.org/10.1371/journal.pgen.1005218

Response to “Ribosome Rescue and Translation Termination at Non-standard Stop Codons by ICT1 in Mammalian Mitochondria”

Zofia Maria Chrzanowska-Lightowlers, Robert Neil Lightowlers

PLOS Genetics: published June 18, 2015 | https://doi.org/10.1371/journal.pgen.1005227

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