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New Articles in PLOS Genetics

Published December 01, 2016 to December 30, 2016

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PLOS Genetics
Volume 12(12) December 2016

View Table of Contents on web site

Editorial

Bringing PLOS Genetics Editors to Preprint Servers
Gregory S. Barsh, Casey M. Bergman, Christopher D. Brown, Nadia D. Singh, Gregory P. Copenhaver

Perspectives

Middle Age Has Its Advantages
Maureen M. Barr

A Hox-Embedded Long Noncoding RNA: Is It All Hot Air?
Licia Selleri, Marisa S. Bartolomei, Wendy A. Bickmore, Lin He, Lisa Stubbs, Wolf Reik, Gregory S. Barsh

Craniofacial Ciliopathies and the Interpretation of Hedgehog Signal Transduction
Karen J. Liu

Review

Tumor Suppressor Genes within Common Fragile Sites Are Active Players in the DNA Damage Response
Idit Hazan, Thomas G. Hofmann, Rami I. Aqeilan

Research Articles

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

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

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

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

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

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

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

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

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

A Novel Rrm3 Function in Restricting DNA Replication via an Orc5-Binding Domain Is Genetically Separable from Rrm3 Function as an ATPase/Helicase in Facilitating Fork Progression
Salahuddin Syed, Claus Desler, Lene J. Rasmussen, Kristina H. Schmidt

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

A Bystander Mechanism Explains the Specific Phenotype of a Broadly Expressed Misfolded Protein
Lauren Klabonski, Ji Zha, Lakshana Senthilkumar, Tali Gidalevitz

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

Ku Binding on Telomeres Occurs at Sites Distal from the Physical Chromosome Ends
Mélanie V. Larcher, Emeline Pasquier, R. Stephen MacDonald, Raymund J. Wellinger

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

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

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

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

Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages
Lauren Gibilisco, Qi Zhou, Shivani Mahajan, Doris Bachtrog

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

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

Intracellular Zn(II) Intoxication Leads to Dysregulation of the PerR Regulon Resulting in Heme Toxicity in Bacillus subtilis
Pete Chandrangsu, John D. Helmann

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

A Kinase-Phosphatase Switch Transduces Environmental Information into a Bacterial Cell Cycle Circuit
Kristina Heinrich, Patrick Sobetzko, Kristina Jonas

Dual Roles for Membrane Association of Drosophila Axin in Wnt Signaling
Zhenghan Wang, Ofelia Tacchelly-Benites, Eungi Yang, Yashi Ahmed

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

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

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

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

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

Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans
Arbel Harpak, Anand Bhaskar, Jonathan K. Pritchard

Hotair Is Dispensible for Mouse Development
Ana Rita Amândio, Anamaria Necsulea, Elisabeth Joye, Bénédicte Mascrez, Denis Duboule

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

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

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

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

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

DNA Methylation Signatures of the Plant Chromomethyltransferases
Quentin Gouil, David C. Baulcombe

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

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

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

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

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

Somatic Mutation Patterns in Hemizygous Genomic Regions Unveil Purifying Selection during Tumor Evolution
Jimmy Van den Eynden, Swaraj Basu, Erik Larsson

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

Olfactory Sensory Neurons Control Dendritic Complexity of Mitral Cells via Notch Signaling
Yuko Muroyama, Atsushi Baba, Motoo Kitagawa, Tetsuichiro Saito

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

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

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

Formal Comments

Comment on "Hotair Is Dispensable for Mouse Development"
Lingjie Li, Jill A. Helms, Howard Y. Chang

Shared Information between Residues Is Sufficient to Detect Pairwise Epistasis in a Protein
Aditi Gupta, Christoph Adami

Epistasis and Entropy
Kristina Crona

Corrections

Correction: The Causative Gene in Chanarian Dorfman Syndrome Regulates Lipid Droplet Homeostasis in C. elegans
Meng Xie, Richard Roy

Correction: 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

Correction: Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation
Andrew D. Hoffmann, Xinan Holly Yang, Ozanna Burnicka-Turek, Joshua D. Bosman, Xiaomeng Ren, Linglin Xie, Jeffrey D. Steimle, Steven A. Vokes, Andrew P. McMahon, Vladimir V. Kalinichenko, Ivan P. Moskowitz

Correction: 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

Correction: Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes
The PLOS Genetics Staff



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