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Table of Contents: December 2016

Pictured is the immunofluorescent staining of 2-month-old ovarian sections showing increased γH2AX in PP6c-depleted oocytes. Blue is DAPI stain. Green is immunofluorescence signal of γH2AX, a marker of DNA double strand breaks. Red is immunofluorescence signal of MVH (mouse VASA homolog), a germ cell marker. Using a genetically modified mouse model with specific deletion of Ppp6c in oocytes from the primordial follicle stage, we show that PP6 plays a critical role in germ cell survival and follicular development by safeguarding the genomic integrity of prophase I-arrested oocytes. See Hu, Meng et al.

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Image Credit: Meng-Wen Hu

Editorial

Bringing PLOS Genetics Editors to Preprint Servers

Gregory S. Barsh, Casey M. Bergman, Christopher D. Brown, Nadia D. Singh, Gregory P. Copenhaver

Review

Research Articles

Hotair Is Dispensible for Mouse Development

Ana Rita Amândio, Anamaria Necsulea, Elisabeth Joye, Bénédicte Mascrez, Denis Duboule

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Structural and Functional Recovery of Sensory Cilia in C. elegans IFT Mutants upon Aging

Astrid Cornils, Ashish K. Maurya, Lauren Tereshko, Julie Kennedy, Andrea G. Brear, Veena Prahlad, Oliver E. Blacque, Piali Sengupta

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The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees

Jian Huang, Chunmei Zhang, Xing Zhao, Zhangjun Fei, KangKang Wan, Zhong Zhang, Xiaoming Pang, Xiao Yin, Yang Bai, Xiaoqing Sun, Lizhi Gao, Ruiqiang Li, Jinbo Zhang, Xingang Li

The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6

Barbora Antosova, Jana Smolikova, Lucie Klimova, Jitka Lachova, Michaela Bendova, Iryna Kozmikova, Ondrej Machon, Zbynek Kozmik

A Bystander Mechanism Explains the Specific Phenotype of a Broadly Expressed Misfolded Protein

Lauren Klabonski, Ji Zha, Lakshana Senthilkumar, Tali Gidalevitz

Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans

Christina M. Kelliher, Adam R. Leman, Crystal S. Sierra, Steven B. Haase

Bilaterian Giant Ankyrins Have a Common Evolutionary Origin and Play a Conserved Role in Patterning the Axon Initial Segment

Timothy Jegla, Michelle M. Nguyen, Chengye Feng, Daniel J. Goetschius, Esteban Luna, Damian B. van Rossum, Bishoy Kamel, Aditya Pisupati, Elliott S. Milner, Melissa M. Rolls

Chronological Lifespan in Yeast Is Dependent on the Accumulation of Storage Carbohydrates Mediated by Yak1, Mck1 and Rim15 Kinases

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

Mutations in the Heme Exporter FLVCR1 Cause Sensory Neurodegeneration with Loss of Pain Perception

Deborah Chiabrando, Marco Castori, Maja di Rocco, Martin Ungelenk, Sebastian Gießelmann, Matteo Di Capua, Annalisa Madeo, Paola Grammatico, Sophie Bartsch, Christian A. Hübner, Fiorella Altruda, Lorenzo Silengo, Emanuela Tolosano, Ingo Kurth

Retinal Expression of the Drosophila eyes absent Gene Is Controlled by Several Cooperatively Acting Cis-regulatory Elements

Bonnie M. Weasner, Brandon P. Weasner, Sarah D. Neuman, Arash Bashirullah, Justin P. Kumar

The Mitochondrial m-AAA Protease Prevents Demyelination and Hair Greying

Shuaiyu Wang, Julie Jacquemyn, Sara Murru, Paola Martinelli, Esther Barth, Thomas Langer, Carien M. Niessen, Elena I. Rugarli

Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages

Lauren Gibilisco, Qi Zhou, Shivani Mahajan, Doris Bachtrog

PCNA-Dependent Cleavage and Degradation of SDE2 Regulates Response to Replication Stress

Ukhyun Jo, Winson Cai, Jingming Wang, Yoojin Kwon, Alan D. D’Andrea, Hyungjin Kim

The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets

Mark P. Keller, Pradyut K. Paul, Mary E. Rabaglia, Donnie S. Stapleton, Kathryn L. Schueler, Aimee Teo Broman, Shuyun Isabella Ye, Ning Leng, Christopher J. Brandon, Elias Chaibub Neto, Christopher L. Plaisier, Shane P. Simonett, Melkam A. Kebede, Gloria M. Sheynkman, Mark A. Klein, Nitin S. Baliga, Lloyd M. Smith, Karl W. Broman, Brian S. Yandell, Christina Kendziorski, Alan D. Attie

Allelic Variation in CXCL16 Determines CD3+ T Lymphocyte Susceptibility to Equine Arteritis Virus Infection and Establishment of Long-Term Carrier State in the Stallion

Sanjay Sarkar, Ernest Bailey, Yun Young Go, R. Frank Cook, Ted Kalbfleisch, John Eberth, R. Lakshman Chelvarajan, Kathleen M. Shuck, Sergey Artiushin, Peter J. Timoney, Udeni B. R. Balasuriya

Identification of a Novel L-rhamnose Uptake Transporter in the Filamentous Fungus Aspergillus niger

Jasper Sloothaak, Dorett I. Odoni, Vitor A. P. Martins dos Santos, Peter J. Schaap, Juan Antonio Tamayo-Ramos

Whole-Organism Developmental Expression Profiling Identifies RAB-28 as a Novel Ciliary GTPase Associated with the BBSome and Intraflagellar Transport

Victor L. Jensen, Stephen Carter, Anna A. W. M. Sanders, Chunmei Li, Julie Kennedy, Tiffany A. Timbers, Jerry Cai, Noemie Scheidel, Breandán N. Kennedy, Ryan D. Morin, Michel R. Leroux, Oliver E. Blacque

Comparative Transcriptomic and Epigenomic Analyses Reveal New Regulators of Murine Brown Adipogenesis

Reinhard Brunmeir, Jingyi Wu, Xu Peng, Sun-Yee Kim, Sofi G. Julien, Qiongyi Zhang, Wei Xie, Feng Xu

The C. elegans Discoidin Domain Receptor DDR-2 Modulates the Met-like RTK–JNK Signaling Pathway in Axon Regeneration

Naoki Hisamoto, Yuki Nagamori, Tatsuhiro Shimizu, Strahil I. Pastuhov, Kunihiro Matsumoto

Gene Expression Differences in Prostate Cancers between Young and Old Men

Yuanchun Ding, Huiqing Wu, Charles Warden, Linda Steele, Xueli Liu, M. van Iterson, Xiwei Wu, Rebecca Nelson, Zheng Liu, Yate-Ching Yuan, Susan L. Neuhausen

Ku Binding on Telomeres Occurs at Sites Distal from the Physical Chromosome Ends

Mélanie V. Larcher, Emeline Pasquier, R. Stephen MacDonald, Raymund J. Wellinger

A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies

Jocelyn Plassais, Laetitia Lagoutte, Solenne Correard, Manon Paradis, Eric Guaguère, Benoit Hédan, Alix Pommier, Nadine Botherel, Marie-Christine Cadiergues, Philippe Pilorge, David Silversides, Maud Bizot, Mark Samuels, Carme Arnan, Rory Johnson, Christophe Hitte, Gilles Salbert, Agnès Méreau, Pascale Quignon, Thomas Derrien, Catherine André

Loss of RMI2 Increases Genome Instability and Causes a Bloom-Like Syndrome

Damien F. Hudson, David J. Amor, Amber Boys, Kathy Butler, Lorna Williams, Tao Zhang, Paul Kalitsis

GW182-Free microRNA Silencing Complex Controls Post-transcriptional Gene Expression during Caenorhabditis elegans Embryogenesis

Guillaume Jannot, Pascale Michaud, Miguel Quévillon Huberdeau, Louis Morel-Berryman, James A. Brackbill, Sandra Piquet, Katherine McJunkin, Kotaro Nakanishi, Martin J. Simard

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  1. Correction: GW182-Free microRNA Silencing Complex Controls Post-transcriptional Gene Expression during Caenorhabditis elegans Embryogenesis

Phosphatidylserine Ameliorates Neurodegenerative Symptoms and Enhances Axonal Transport in a Mouse Model of Familial Dysautonomia

Shiran Naftelberg, Ziv Abramovitch, Shani Gluska, Sivan Yannai, Yuvraj Joshi, Maya Donyo, Keren Ben-Yaakov, Tal Gradus, Jonathan Zonszain, Chen Farhy, Ruth Ashery-Padan, Eran Perlson, Gil Ast

Bypass of Candida albicans Filamentation/Biofilm Regulators through Diminished Expression of Protein Kinase Cak1

Carol A. Woolford, Katherine Lagree, Wenjie Xu, Tatyana Aleynikov, Hema Adhikari, Hiram Sanchez, Paul J. Cullen, Frederick Lanni, David R. Andes, Aaron P. Mitchell

Unique Function of the Bacterial Chromosome Segregation Machinery in Apically Growing Streptomyces - Targeting the Chromosome to New Hyphal Tubes and its Anchorage at the Tips

Agnieszka Kois-Ostrowska, Agnieszka Strzałka, Natalia Lipietta, Emma Tilley, Jolanta Zakrzewska-Czerwińska, Paul Herron, Dagmara Jakimowicz

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

Sarah R. Smith, Jeroen T. F. Gillard, Adam B. Kustka, John P. McCrow, Jonathan H. Badger, Hong Zheng, Ashley M. New, Chris L. Dupont, Toshihiro Obata, Alisdair R. Fernie, Andrew E. Allen

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  1. Correction: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data

Jianxin Shi, Ju-Hyun Park, Jubao Duan, Sonja T. Berndt, Winton Moy, Kai Yu, Lei Song, William Wheeler, Xing Hua, Debra Silverman, Montserrat Garcia-Closas, Chao Agnes Hsiung, Jonine D. Figueroa, Victoria K. Cortessis, Núria Malats, Margaret R. Karagas, Paolo Vineis, I-Shou Chang, Dongxin Lin, Baosen Zhou, Adeline Seow, Keitaro Matsuo, Yun-Chul Hong, Neil E. Caporaso, Brian Wolpin, Eric Jacobs, Gloria M. Petersen, Alison P. Klein, Donghui Li, Harvey Risch, Alan R. Sanders, Li Hsu, Robert E. Schoen, Hermann Brenner, MGS (Molecular Genetics of Schizophrenia) GWAS Consortium, GECCO (The Genetics and Epidemiology of Colorectal Cancer Consortium), The GAME-ON/TRICL (Transdisciplinary Research in Cancer of the Lung) GWAS Consortium, PRACTICAL (PRostate cancer AssoCiation group To Investigate Cancer Associated aLterations) Consortium, PanScan Consortium, The GAME-ON/ELLIPSE Consortium, Rachael Stolzenberg-Solomon, Pablo Gejman, Qing Lan, Nathaniel Rothman, Laufey T. Amundadottir, Maria Teresa Landi, Douglas F. Levinson, Stephen J. Chanock, Nilanjan Chatterjee

Dual Roles for Membrane Association of Drosophila Axin in Wnt Signaling

Zhenghan Wang, Ofelia Tacchelly-Benites, Eungi Yang, Yashi Ahmed

NUCLEAR FACTOR Y, Subunit A (NF-YA) Proteins Positively Regulate Flowering and Act Through FLOWERING LOCUS T

Chamindika L. Siriwardana, Nerina Gnesutta, Roderick W. Kumimoto, Daniel S. Jones, Zachary A. Myers, Roberto Mantovani, Ben F. Holt III

Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria

Silvia Ardissone, Peter Redder, Giancarlo Russo, Antonio Frandi, Coralie Fumeaux, Andrea Patrignani, Ralph Schlapbach, Laurent Falquet, Patrick H. Viollier

Enrichment of Targetable Mutations in the Relapsed Neuroblastoma Genome

Olivia M. Padovan-Merhar, Pichai Raman, Irina Ostrovnaya, Karthik Kalletla, Kaitlyn R. Rubnitz, Eric M. Sanford, Siraj M. Ali, Vincent A. Miller, Yael P. Mossé, Meaghan P. Granger, Brian Weiss, John M. Maris, Shakeel Modak

Mitochondria and Caspases Tune Nmnat-Mediated Stabilization to Promote Axon Regeneration

Li Chen, Derek M. Nye, Michelle C. Stone, Alexis T. Weiner, Kyle W. Gheres, Xin Xiong, Catherine A. Collins, Melissa M. Rolls

Interaction of Prions Causes Heritable Traits in Saccharomyces cerevisiae

Anton A. Nizhnikov, Tatyana A. Ryzhova, Kirill V. Volkov, Sergey P. Zadorsky, Julia V. Sopova, Sergey G. Inge-Vechtomov, Alexey P. Galkin

Elevated Fibroblast Growth Factor Signaling Is Critical for the Pathogenesis of the Dwarfism in Evc2/Limbin Mutant Mice

Honghao Zhang, Nobuhiro Kamiya, Takehito Tsuji, Haruko Takeda, Greg Scott, Sudha Rajderkar, Manas K. Ray, Yoshiyuki Mochida, Benjamin Allen, Veronique Lefebvre, Irene H. Hung, David M. Ornitz, Tetsuo Kunieda, Yuji Mishina

Extensive Regulation of Diurnal Transcription and Metabolism by Glucocorticoids

Benjamin D. Weger, Meltem Weger, Benjamin Görling, Andrea Schink, Cédric Gobet, Céline Keime, Gernot Poschet, Bernard Jost, Nils Krone, Rüdiger Hell, Frédéric Gachon, Burkhard Luy, Thomas Dickmeis

Protein Phosphatase 6 Protects Prophase I-Arrested Oocytes by Safeguarding Genomic Integrity

Meng-Wen Hu, Tie-Gang Meng, Zong-Zhe Jiang, Ming-Zhe Dong, Heide Schatten, Xingzhi Xu, Zhen-Bo Wang, Qing-Yuan Sun

Olfactory Sensory Neurons Control Dendritic Complexity of Mitral Cells via Notch Signaling

Yuko Muroyama, Atsushi Baba, Motoo Kitagawa, Tetsuichiro Saito

PERK Is a Haploinsufficient Tumor Suppressor: Gene Dose Determines Tumor-Suppressive Versus Tumor Promoting Properties of PERK in Melanoma

Dariusz Pytel, Yan Gao, Katarzyna Mackiewicz, Yuliya V. Katlinskaya, Kirk A. Staschke, Maria C. G. Paredes, Akihiro Yoshida, Shuo Qie, Gao Zhang, Olga S. Chajewski, Lawrence Wu, Ireneusz Majsterek, Meenhard Herlyn, Serge Y. Fuchs, J. Alan Diehl

Tbx5 Buffers Inherent Left/Right Asymmetry Ensuring Symmetric Forelimb Formation

Fatima A. Sulaiman, Satoko Nishimoto, George R. F. Murphy, Anna Kucharska, Natalie C. Butterfield, Ruth Newbury-Ecob, Malcolm P. O. Logan

A Kinase-Phosphatase Switch Transduces Environmental Information into a Bacterial Cell Cycle Circuit

Kristina Heinrich, Patrick Sobetzko, Kristina Jonas

On the Spatial Organization of mRNA, Plasmids, and Ribosomes in a Bacterial Host Overexpressing Membrane Proteins

Lieke A. van Gijtenbeek, Andrew Robinson, Antoine M. van Oijen, Bert Poolman, Jan Kok

DNA Methylation Signatures of the Plant Chromomethyltransferases

Quentin Gouil, David C. Baulcombe

A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans

Yael Bar-Lavan, Netta Shemesh, Shiran Dror, Rivka Ofir, Esti Yeger-Lotem, Anat Ben-Zvi

Deep Reads

Deep Reads: Favorites from a Few Different Shelves

Bruce A. Hamilton