September 2016

c-Fos overexpression (right image) in the ovary of the fruitfly (Drosophila melanogaster) results in enlarged tissue volume and germ cell developmental arrest. Pictured are an ovary from a wild-type (left) fruitfly and an ovary from a fruitfly that overexpresses the c-Fos transgene. Blue is DAPI stain. Green is immunofluorescence signal of Vasa, a germ cell marker. White bar is 100 um scale bar. Klein et al. uncovered that Piwi and non-coding Piwi-interacting RNAs repress c-Fos to regulate ovarian tissue morphogenesis, germ cell development, and animal fertility. Replacement of the 3’ untranslated region of the c-Fos mRNA, which originates Piwi-interacting RNAs, results in c-Fos overexpression, disorganized ovarian cells, arrest in germ cell maturation, and complete animal infertility. See Klein et al.

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Image Credit: Jonathon D. Klein and Victoria Frohlich, using a Zeiss LightSheet Z.1 system.

Perspectives

Reactive Oxygen Species: From Harmful Molecules to Fine-Tuning Regulators of Stem Cell Niche Maintenance

Juan Carlos del Pozo

PLOS Genetics: published September 1, 2016 | https://doi.org/10.1371/journal.pgen.1006251

The Clock Is Ticking: Countdown to Metastases

Linda D. Siracusa, Karen M. Bussard

PLOS Genetics: published September 22, 2016 | https://doi.org/10.1371/journal.pgen.1006299

Review

Acetylation Reader Proteins: Linking Acetylation Signaling to Genome Maintenance and Cancer

Fade Gong, Li-Ya Chiu, Kyle M. Miller

PLOS Genetics: published September 15, 2016 | https://doi.org/10.1371/journal.pgen.1006272

Research Articles

A P-Loop NTPase Regulates Quiescent Center Cell Division and Distal Stem Cell Identity through the Regulation of ROS Homeostasis in Arabidopsis Root

Qianqian Yu, Huiyu Tian, Kun Yue, Jiajia Liu, Bing Zhang, Xugang Li, Zhaojun Ding

PLOS Genetics: published September 1, 2016 | https://doi.org/10.1371/journal.pgen.1006175

Tuning PAK Activity to Rescue Abnormal Myelin Permeability in HNPP

Bo Hu, Sezgi Arpag, Xuebao Zhang, Wiebke Möbius, Hauke Werner, Gina Sosinsky, Mark Ellisman, Yang Zhang, Audra Hamilton, Jonathan Chernoff, Jun Li

PLOS Genetics: published September 1, 2016 | https://doi.org/10.1371/journal.pgen.1006290

DMRT1 Is Required for Mouse Spermatogonial Stem Cell Maintenance and Replenishment

Teng Zhang, Jon Oatley, Vivian J. Bardwell, David Zarkower

PLOS Genetics: published September 1, 2016 | https://doi.org/10.1371/journal.pgen.1006293

dBRWD3 Regulates Tissue Overgrowth and Ectopic Gene Expression Caused by Polycomb Group Mutations

Hsueh-Tzu Shih, Wei-Yu Chen, Kwei-Yan Liu, Zong-Siou Shih, Yi-Jyun Chen, Paul-Chen Hsieh, Kuan-Lin Kuo, Kuo-How Huang, Pang-Hung Hsu, Ya-Wen Liu, Shih-Peng Chan, Hsiu-Hsiang Lee, Yu-Chen Tsai, June-Tai Wu

PLOS Genetics: published September 2, 2016 | https://doi.org/10.1371/journal.pgen.1006262

Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions

Lai H. Wong, Sunita Sinha, Julien R. Bergeron, Joseph C. Mellor, Guri Giaever, Patrick Flaherty, Corey Nislow

PLOS Genetics: published September 2, 2016 | https://doi.org/10.1371/journal.pgen.1006275

Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

Michalis Barkoulas, Amhed M. Vargas Velazquez, Alexandre E. Peluffo, Marie-Anne Félix

PLOS Genetics: published September 2, 2016 | https://doi.org/10.1371/journal.pgen.1006278

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity

Barbara Mair, Tomasz Konopka, Claudia Kerzendorfer, Katia Sleiman, Sejla Salic, Violeta Serra, Markus K. Muellner, Vasiliki Theodorou, Sebastian M. B. Nijman

PLOS Genetics: published September 2, 2016 | https://doi.org/10.1371/journal.pgen.1006279

Whole Exome Sequencing in Atrial Fibrillation

Steven A. Lubitz, Jennifer A. Brody, Nathan A. Bihlmeyer, Carolina Roselli, Lu-Chen Weng, Ingrid E. Christophersen, Alvaro Alonso, Eric Boerwinkle, Richard A. Gibbs, Joshua C. Bis, NHLBI GO Exome Sequencing Project, L. Adrienne Cupples, Peter J. Mohler, Deborah A. Nickerson, Donna Muzny, Marco V. Perez, Bruce M. Psaty, Elsayed Z. Soliman, Nona Sotoodehnia, Kathryn L. Lunetta, Emelia J. Benjamin, Susan R. Heckbert, Dan E. Arking, Patrick T. Ellinor, Honghuang Lin

PLOS Genetics: published September 2, 2016 | https://doi.org/10.1371/journal.pgen.1006284

DNA Replication Control Is Linked to Genomic Positioning of Control Regions in Escherichia coli

Jakob Frimodt-Møller, Godefroid Charbon, Karen A. Krogfelt, Anders Løbner-Olesen

PLOS Genetics: published September 2, 2016 | https://doi.org/10.1371/journal.pgen.1006286

Using Genetic Distance to Infer the Accuracy of Genomic Prediction

Marco Scutari, Ian Mackay, David Balding

PLOS Genetics: published September 2, 2016 | https://doi.org/10.1371/journal.pgen.1006288

Genetic Evidence That Captured Retroviral Envelope syncytins Contribute to Myoblast Fusion and Muscle Sexual Dimorphism in Mice

François Redelsperger, Najat Raddi, Agathe Bacquin, Cécile Vernochet, Virginie Mariot, Vincent Gache, Nicolas Blanchard-Gutton, Stéphanie Charrin, Laurent Tiret, Julie Dumonceaux, Anne Dupressoir, Thierry Heidmann

PLOS Genetics: published September 2, 2016 | https://doi.org/10.1371/journal.pgen.1006289

Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster

Hangnoh Lee, Dong-Yeon Cho, Cale Whitworth, Robert Eisman, Melissa Phelps, John Roote, Thomas Kaufman, Kevin Cook, Steven Russell, Teresa Przytycka, Brian Oliver

PLOS Genetics: published September 6, 2016 | https://doi.org/10.1371/journal.pgen.1006295

The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σ^V Activation

Jessica L. Hastie, Kyle B. Williams, Lindsey L. Bohr, Jon C. Houtman, Lokesh Gakhar, Craig D. Ellermeier

PLOS Genetics: published September 7, 2016 | https://doi.org/10.1371/journal.pgen.1006287

RNA-Binding Protein FXR1 Regulates p21 and TERC RNA to Bypass p53-Mediated Cellular Senescence in OSCC

Mrinmoyee Majumder, Reniqua House, Nallasivam Palanisamy, Shuo Qie, Terrence A. Day, David Neskey, J. Alan Diehl, Viswanathan Palanisamy

PLOS Genetics: published September 8, 2016 | https://doi.org/10.1371/journal.pgen.1006306

Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity

Karin R. McDonald, Amanda J. Guise, Parham Pourbozorgi-Langroudi, Ileana M. Cristea, Virginia A. Zakian, John A. Capra, Nasim Sabouri

PLOS Genetics: published September 9, 2016 | https://doi.org/10.1371/journal.pgen.1006238

mSWI/SNF (BAF) Complexes Are Indispensable for the Neurogenesis and Development of Embryonic Olfactory Epithelium

Christina Bachmann, Huong Nguyen, Joachim Rosenbusch, Linh Pham, Tamara Rabe, Megha Patwa, Godwin Sokpor, Rho H. Seong, Ruth Ashery-Padan, Ahmed Mansouri, Anastassia Stoykova, Jochen F. Staiger, Tran Tuoc

PLOS Genetics: published September 9, 2016 | https://doi.org/10.1371/journal.pgen.1006274

A Taz1- and Microtubule-Dependent Regulatory Relationship between Telomere and Centromere Positions in Bouquet Formation Secures Proper Meiotic Divisions

Kazuhiro Katsumata, Ami Hirayasu, Junpei Miyoshi, Eriko Nishi, Kento Ichikawa, Kazuki Tateho, Airi Wakuda, Hirotada Matsuhara, Ayumu Yamamoto

PLOS Genetics: published September 9, 2016 | https://doi.org/10.1371/journal.pgen.1006304

The PU.1-Modulated MicroRNA-22 Is a Regulator of Monocyte/Macrophage Differentiation and Acute Myeloid Leukemia

Chao Shen, Ming-Tai Chen, Xin-Hua Zhang, Xiao-Lin Yin, Hong-Mei Ning, Rui Su, Hai-Shuang Lin, Li Song, Fang Wang, Yan-Ni Ma, Hua-Lu Zhao, Jia Yu, Jun-Wu Zhang

PLOS Genetics: published September 12, 2016 | https://doi.org/10.1371/journal.pgen.1006259

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

Alan McNally, Yaara Oren, Darren Kelly, Ben Pascoe, Steven Dunn, Tristan Sreecharan, Minna Vehkala, Niko Välimäki, Michael B. Prentice, Amgad Ashour, Oren Avram, Tal Pupko, Ulrich Dobrindt, Ivan Literak, Sebastian Guenther, Katharina Schaufler, Lothar H. Wieler, Zong Zhiyong, Samuel K. Sheppard, James O. McInerney, Jukka Corander

PLOS Genetics: published September 12, 2016 | https://doi.org/10.1371/journal.pgen.1006280

Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly

Hanqian Mao, John J. McMahon, Yi-Hsuan Tsai, Zefeng Wang, Debra L. Silver

PLOS Genetics: published September 12, 2016 | https://doi.org/10.1371/journal.pgen.1006282

Oligomerization of SCF^TIR1 Is Essential for Aux/IAA Degradation and Auxin Signaling in Arabidopsis

Mohammad H. Dezfulian, Espanta Jalili, Don Karl A. Roberto, Britney L. Moss, Kerry Khoo, Jennifer L. Nemhauser, William L. Crosby

PLOS Genetics: published September 12, 2016 | https://doi.org/10.1371/journal.pgen.1006301

The Multivesicular Bodies (MVBs)-Localized AAA ATPase LRD6-6 Inhibits Immunity and Cell Death Likely through Regulating MVBs-Mediated Vesicular Trafficking in Rice

Xiaobo Zhu, Junjie Yin, Sihui Liang, Ruihong Liang, Xiaogang Zhou, Zhixiong Chen, Wen Zhao, Jing Wang, Weitao Li, Min He, Can Yuan, Koji Miyamoto, Bingtian Ma, Jichun Wang, Peng Qin, Weilan Chen, Yuping Wang, Wenming Wang, Xianjun Wu, Hisakazu Yamane, Lihuang Zhu, Shigui Li, Xuewei Chen

PLOS Genetics: published September 12, 2016 | https://doi.org/10.1371/journal.pgen.1006311

Epistatic Gene-Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium

Shefali Setia Verma, Jessica N. Cooke Bailey, Anastasia Lucas, Yuki Bradford, James G. Linneman, Michael A. Hauser, Louis R. Pasquale, Peggy L. Peissig, Murray H. Brilliant, Catherine A. McCarty, Jonathan L. Haines, Janey L. Wiggs, Tamara R. Vrabec, Gerard Tromp, Marylyn D. Ritchie, eMERGE Network, NEIGHBOR Consortium

PLOS Genetics: published September 13, 2016 | https://doi.org/10.1371/journal.pgen.1006186

c-Fos Repression by Piwi Regulates Drosophila Ovarian Germline Formation and Tissue Morphogenesis

Jonathon D. Klein, Chunxu Qu, Xiaoyang Yang, Yiping Fan, Chunlao Tang, Jamy C. Peng

PLOS Genetics: published September 13, 2016 | https://doi.org/10.1371/journal.pgen.1006281

Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana

Xin-Yuan Huang, Dai-Yin Chao, Anna Koprivova, John Danku, Markus Wirtz, Steffen Müller, Francisco J. Sandoval, Hermann Bauwe, Sanja Roje, Brian Dilkes, Rüdiger Hell, Stanislav Kopriva, David E Salt

PLOS Genetics: published September 13, 2016 | https://doi.org/10.1371/journal.pgen.1006298

Altered mRNA Splicing, Chondrocyte Gene Expression and Abnormal Skeletal Development due to SF3B4 Mutations in Rodriguez Acrofacial Dysostosis

Felipe Marques, Jessica Tenney, Ivan Duran, Jorge Martin, Lisette Nevarez, Robert Pogue, Deborah Krakow, Daniel H. Cohn, Bing Li

PLOS Genetics: published September 13, 2016 | https://doi.org/10.1371/journal.pgen.1006307

The Rheumatoid Arthritis Risk Variant CCR6DNP Regulates CCR6 via PARP-1

Gang Li, Pierre Cunin, Di Wu, Dorothée Diogo, Yu Yang, Yukinori Okada, Robert M. Plenge, Peter A. Nigrovic

PLOS Genetics: published September 14, 2016 | https://doi.org/10.1371/journal.pgen.1006292

The MaoP/maoS Site-Specific System Organizes the Ori Region of the E. coli Chromosome into a Macrodomain

Michèle Valens, Axel Thiel, Frédéric Boccard

PLOS Genetics: published September 14, 2016 | https://doi.org/10.1371/journal.pgen.1006309

The Contribution of Mosaic Variants to Autism Spectrum Disorder

Donald Freed, Jonathan Pevsner

PLOS Genetics: published September 15, 2016 | https://doi.org/10.1371/journal.pgen.1006245

The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis

Bradley J Main, Yoosook Lee, Heather M. Ferguson, Katharina S. Kreppel, Anicet Kihonda, Nicodem J. Govella, Travis C. Collier, Anthony J. Cornel, Eleazar Eskin, Eun Yong Kang, Catelyn C. Nieman, Allison M. Weakley, Gregory C. Lanzaro

PLOS Genetics: published September 15, 2016 | https://doi.org/10.1371/journal.pgen.1006303

Loss of the Greatwall Kinase Weakens the Spindle Assembly Checkpoint

M. Kasim Diril, Xavier Bisteau, Mayumi Kitagawa, Matias J. Caldez, Sheena Wee, Jayantha Gunaratne, Sang Hyun Lee, Philipp Kaldis

PLOS Genetics: published September 15, 2016 | https://doi.org/10.1371/journal.pgen.1006310

A Recombination Directionality Factor Controls the Cell Type-Specific Activation of σ^K and the Fidelity of Spore Development in Clostridium difficile

Mónica Serrano, Nicolas Kint, Fátima C. Pereira, Laure Saujet, Pierre Boudry, Bruno Dupuy, Adriano O. Henriques, Isabelle Martin-Verstraete

PLOS Genetics: published September 15, 2016 | https://doi.org/10.1371/journal.pgen.1006312

XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans

Takashi S. Miki, Sarah H. Carl, Michael B. Stadler, Helge Großhans

PLOS Genetics: published September 15, 2016 | https://doi.org/10.1371/journal.pgen.1006313

Bmp15 Is an Oocyte-Produced Signal Required for Maintenance of the Adult Female Sexual Phenotype in Zebrafish

Daniel B. Dranow, Kevin Hu, April M. Bird, S. Terese Lawry, Melissa T. Adams, Angelica Sanchez, James F. Amatruda, Bruce W. Draper

PLOS Genetics: published September 19, 2016 | https://doi.org/10.1371/journal.pgen.1006323

Sex-Specific Selection and Sex-Biased Gene Expression in Humans and Flies

Changde Cheng, Mark Kirkpatrick

PLOS Genetics: published September 22, 2016 | https://doi.org/10.1371/journal.pgen.1006170

The Circadian Rhythm Gene Arntl2 Is a Metastasis Susceptibility Gene for Estrogen Receptor-Negative Breast Cancer

Ngoc-Han Ha, Jirong Long, Qiuyin Cai, Xiao Ou Shu, Kent W. Hunter

PLOS Genetics: published September 22, 2016 | https://doi.org/10.1371/journal.pgen.1006267

The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts

Maléne E Lindholm, Stefania Giacomello, Beata Werne Solnestam, Helene Fischer, Mikael Huss, Sanela Kjellqvist, Carl Johan Sundberg

PLOS Genetics: published September 22, 2016 | https://doi.org/10.1371/journal.pgen.1006294

Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome

Laura S. Burrack, Hannah F. Hutton, Kathleen J. Matter, Shelly Applen Clancey, Ivan Liachko, Alexandra E. Plemmons, Amrita Saha, Erica A. Power, Breanna Turman, Mathuravani Aaditiyaa Thevandavakkam, Ferhat Ay, Maitreya J. Dunham, Judith Berman

PLOS Genetics: published September 23, 2016 | https://doi.org/10.1371/journal.pgen.1006317

A Broad Set of Chromatin Factors Influences Splicing

Eric Allemand, Michael P. Myers, Jose Garcia-Bernardo, Annick Harel-Bellan, Adrian R. Krainer, Christian Muchardt

PLOS Genetics: published September 23, 2016 | https://doi.org/10.1371/journal.pgen.1006318

Drosophila TDP-43 RNA-Binding Protein Facilitates Association of Sister Chromatid Cohesion Proteins with Genes, Enhancers and Polycomb Response Elements

Amanda Swain, Ziva Misulovin, Michelle Pherson, Maria Gause, Kathie Mihindukulasuriya, Ryan A Rickels, Ali Shilatifard, Dale Dorsett

PLOS Genetics: published September 23, 2016 | https://doi.org/10.1371/journal.pgen.1006331

Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

Yuheng Huang, Aneil F. Agrawal

PLOS Genetics: published September 23, 2016 | https://doi.org/10.1371/journal.pgen.1006336

PARAQUAT TOLERANCE3 Is an E3 Ligase That Switches off Activated Oxidative Response by Targeting Histone-Modifying PROTEIN METHYLTRANSFERASE4b

Chao Luo, Xiao-Teng Cai, Jin Du, Tao-Lan Zhao, Peng-Fei Wang, Ping-Xia Zhao, Rui Liu, Qi Xie, Xiao-Feng Cao, Cheng-Bin Xiang

PLOS Genetics: published September 27, 2016 | https://doi.org/10.1371/journal.pgen.1006332

Dose-Dependent Regulation of Alternative Splicing by MBNL Proteins Reveals Biomarkers for Myotonic Dystrophy

Stacey D. Wagner, Adam J. Struck, Riti Gupta, Dylan R. Farnsworth, Amy E. Mahady, Katy Eichinger, Charles A. Thornton, Eric T. Wang, J. Andrew Berglund

PLOS Genetics: published September 28, 2016 | https://doi.org/10.1371/journal.pgen.1006316

Arabidopsis CaM1 and CaM4 Promote Nitric Oxide Production and Salt Resistance by Inhibiting S-Nitrosoglutathione Reductase via Direct Binding

Shuo Zhou, Lixiu Jia, Hongye Chu, Dan Wu, Xuan Peng, Xu Liu, Jiaojiao Zhang, Junfeng Zhao, Kunming Chen, Liqun Zhao

PLOS Genetics: published September 29, 2016 | https://doi.org/10.1371/journal.pgen.1006255

Drosophila Adaptation to Viral Infection through Defensive Symbiont Evolution

Vitor G. Faria, Nelson E. Martins, Sara Magalhães, Tânia F. Paulo, Viola Nolte, Christian Schlötterer, Élio Sucena, Luis Teixeira

PLOS Genetics: published September 29, 2016 | https://doi.org/10.1371/journal.pgen.1006297

NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana

Zachary A. Myers, Roderick W. Kumimoto, Chamindika L. Siriwardana, Krystal K. Gayler, Jan R. Risinger, Daniela Pezzetta, Ben F. Holt III

PLOS Genetics: published September 29, 2016 | https://doi.org/10.1371/journal.pgen.1006333

Prion Aggregates Are Recruited to the Insoluble Protein Deposit (IPOD) via Myosin 2-Based Vesicular Transport

Rajesh Kumar, Peter P. Nawroth, Jens Tyedmers

PLOS Genetics: published September 30, 2016 | https://doi.org/10.1371/journal.pgen.1006324

Mutations in Nonessential eIF3k and eIF3l Genes Confer Lifespan Extension and Enhanced Resistance to ER Stress in Caenorhabditis elegans

Douglas J. Cattie, Claire E. Richardson, Kirthi C. Reddy, Elan M. Ness-Cohn, Rita Droste, Mary K. Thompson, Wendy V. Gilbert, Dennis H. Kim

PLOS Genetics: published September 30, 2016 | https://doi.org/10.1371/journal.pgen.1006326

Dnmt3a Is a Haploinsufficient Tumor Suppressor in CD8+ Peripheral T Cell Lymphoma

Staci L. Haney, G. Michael Upchurch, Jana Opavska, David Klinkebiel, Ryan A. Hlady, Sohini Roy, Samikshan Dutta, Kaustubh Datta, Rene Opavsky

PLOS Genetics: published September 30, 2016 | https://doi.org/10.1371/journal.pgen.1006334

Widespread Shortening of 3’ Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection

Athma A. Pai, Golshid Baharian, Ariane Pagé Sabourin, Jessica F. Brinkworth, Yohann Nédélec, Joseph W. Foley, Jean-Christophe Grenier, Katherine J. Siddle, Anne Dumaine, Vania Yotova, Zachary P. Johnson, Robert E. Lanford, Christopher B. Burge, Luis B. Barreiro

PLOS Genetics: published September 30, 2016 | https://doi.org/10.1371/journal.pgen.1006338

Mtu1-Mediated Thiouridine Formation of Mitochondrial tRNAs Is Required for Mitochondrial Translation and Is Involved in Reversible Infantile Liver Injury

Yong Wu, Fan-Yan Wei, Layla Kawarada, Takeo Suzuki, Kimi Araki, Yoshihiro Komohara, Atsushi Fujimura, Taku Kaitsuka, Motohiro Takeya, Yuichi Oike, Tsutomu Suzuki, Kazuhito Tomizawa

PLOS Genetics: published September 30, 2016 | https://doi.org/10.1371/journal.pgen.1006355

ATX-2, the C. elegans Ortholog of Human Ataxin-2, Regulates Centrosome Size and Microtubule Dynamics

Michael D. Stubenvoll, Jeffrey C. Medley, Miranda Irwin, Mi Hye Song

PLOS Genetics: published September 30, 2016 | https://doi.org/10.1371/journal.pgen.1006370

Cover

c-Fos regulation by piwi in the Drosophila ovary.

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