November 2016

Skeletons contain hundreds of joints that are crucial for movement of different bones in the body. Regulatory studies of a key developmental and arthritis risk factor gene (Gdf5) have now identified a battery of distinct non-coding enhancers that control expression in particular joints, including specific joints in the head, shoulders, elbows, hips, and knees (left transgenic reporter mouse embryo), versus fingers and toes in the forelimb and hindlimb (right transgenic embryo carrying a different construct). Changes in individual joint control sequences may underlie localized evolutionary changes in vertebrate limbs, or susceptibility to arthritis in certain parts of the skeleton. See Chen, Capellini et al.

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Image Credit: Chen, Capellini et al.

Perspectives

The Rise of FXR1: Escaping Cellular Senescence in Head and Neck Squamous Cell Carcinoma

Erlinda Fernández, Frédérick A. Mallette

PLOS Genetics: published November 3, 2016 | https://doi.org/10.1371/journal.pgen.1006344

The Mighty Fruit Fly Moves into Outbred Genetics

Ewan Birney

PLOS Genetics: published November 3, 2016 | https://doi.org/10.1371/journal.pgen.1006388

Suggestions from Geroscience for the Genetics of Age-Related Diseases

Claudio Franceschi, Paolo Garagnani

PLOS Genetics: published November 10, 2016 | https://doi.org/10.1371/journal.pgen.1006399

A Helping Hand: RNA-Binding Proteins Guide Gene-Binding Choices by Cohesin Complexes

Alyssa N. Coyne, Daniela C. Zarnescu

PLOS Genetics: published November 17, 2016 | https://doi.org/10.1371/journal.pgen.1006419

Research Articles

Pleiotropic Associations of Allelic Variants in a 2q22 Region with Risks of Major Human Diseases and Mortality

Alexander M. Kulminski, Liang He, Irina Culminskaya, Yury Loika, Yelena Kernogitski, Konstantin G. Arbeev, Elena Loiko, Liubov Arbeeva, Olivia Bagley, Matt Duan, Arseniy Yashkin, Fang Fang, Mikhail Kovtun, Svetlana V. Ukraintseva, Deqing Wu, Anatoliy I. Yashin

PLOS Genetics: published November 10, 2016 | https://doi.org/10.1371/journal.pgen.1006314

Multi-nucleotide de novo Mutations in Humans

Søren Besenbacher, Patrick Sulem, Agnar Helgason, Hannes Helgason, Helgi Kristjansson, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Olafur Th. Magnusson, Unnur Thorsteinsdottir, Gisli Masson, Augustine Kong, Daniel F. Gudbjartsson, Kari Stefansson

PLOS Genetics: published November 15, 2016 | https://doi.org/10.1371/journal.pgen.1006315

High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop

Chenxi Qiu, Olivia C. Erinne, Jui M. Dave, Ping Cui, Huiyan Jin, Nandhini Muthukrishnan, Leung K. Tang, Sabareesh Ganesh Babu, Kenny C. Lam, Paul J. Vandeventer, Ralf Strohner, Jan Van den Brulle, Sing-Hoi Sze, Craig D. Kaplan

PLOS Genetics: published November 29, 2016 | https://doi.org/10.1371/journal.pgen.1006321

Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-Binding Regions in BR-C

Anna Hitrik, Malka Popliker, Dana Gancz, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Amos Tanay, Lilach Gilboa

PLOS Genetics: published November 15, 2016 | https://doi.org/10.1371/journal.pgen.1006330

The Strength of Selection against Neanderthal Introgression

Ivan Juric, Simon Aeschbacher, Graham Coop

PLOS Genetics: published November 8, 2016 | https://doi.org/10.1371/journal.pgen.1006340

Craniofacial Ciliopathies Reveal Specific Requirements for GLI Proteins during Development of the Facial Midline

Ching-Fang Chang, Ya-Ting Chang, Grethel Millington, Samantha A. Brugmann

PLOS Genetics: published November 1, 2016 | https://doi.org/10.1371/journal.pgen.1006351

Experimental Evolution of Metabolic Dependency in Bacteria

Glen D’Souza, Christian Kost

PLOS Genetics: published November 4, 2016 | https://doi.org/10.1371/journal.pgen.1006364

High-Resolution Genetics Identifies the Lipid Transfer Protein Sec14p as Target for Antifungal Ergolines

Ireos Filipuzzi, Simona Cotesta, Francesca Perruccio, Britta Knapp, Yue Fu, Christian Studer, Verena Pries, Ralph Riedl, Stephen B. Helliwell, Katarina T. Petrovic, N. Rao Movva, Dominique Sanglard, Jianshi Tao, Dominic Hoepfner

PLOS Genetics: published November 17, 2016 | https://doi.org/10.1371/journal.pgen.1006374

Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes

H. Charlotte van der Does, Like Fokkens, Ally Yang, Sarah M. Schmidt, Léon Langereis, Joanna M. Lukasiewicz, Timothy R. Hughes, Martijn Rep

PLOS Genetics: published November 17, 2016 | https://doi.org/10.1371/journal.pgen.1006401

Programmed Minichromosome Elimination as a Mechanism for Somatic Genome Reduction in Tetrahymena thermophila

Chih-Yi Gabriela Lin, I-Ting Lin, Meng-Chao Yao

PLOS Genetics: published November 2, 2016 | https://doi.org/10.1371/journal.pgen.1006403

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species

Markus S. Schröder, Kontxi Martinez de San Vicente, Tâmara H. R. Prandini, Stephen Hammel, Desmond G. Higgins, Eduardo Bagagli, Kenneth H. Wolfe, Geraldine Butler

PLOS Genetics: published November 2, 2016 | https://doi.org/10.1371/journal.pgen.1006404

Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns

Tal Cohen, Liron Levin, Dan Mishmar

PLOS Genetics: published November 3, 2016 | https://doi.org/10.1371/journal.pgen.1006407

Experimental Evolution Reveals Interplay between Sch9 and Polyploid Stability in Yeast

Yi-Jin Lu, Krishna B. S. Swamy, Jun-Yi Leu

PLOS Genetics: published November 3, 2016 | https://doi.org/10.1371/journal.pgen.1006409

Complex Breakpoints and Template Switching Associated with Non-canonical Termination of Homologous Recombination in Mammalian Cells

Andrea J. Hartlerode, Nicholas A. Willis, Anbazhagan Rajendran, John P. Manis, Ralph Scully

PLOS Genetics: published November 10, 2016 | https://doi.org/10.1371/journal.pgen.1006410

A Novel Tiller Angle Gene, TAC3, together with TAC1 and D2 Largely Determine the Natural Variation of Tiller Angle in Rice Cultivars

Haijiao Dong, Hu Zhao, Weibo Xie, Zhongmin Han, Guangwei Li, Wen Yao, Xufeng Bai, Yong Hu, Zilong Guo, Kai Lu, Lin Yang, Yongzhong Xing

PLOS Genetics: published November 4, 2016 | https://doi.org/10.1371/journal.pgen.1006412

Bottom-up Assembly of the Phytochrome Network

Maximiliano Sánchez-Lamas, Christian D. Lorenzo, Pablo D. Cerdán

PLOS Genetics: published November 7, 2016 | https://doi.org/10.1371/journal.pgen.1006413

Budding Yeast Rif1 Controls Genome Integrity by Inhibiting rDNA Replication

Maksym Shyian, Stefano Mattarocci, Benjamin Albert, Lukas Hafner, Aleksandra Lezaja, Michael Costanzo, Charlie Boone, David Shore

PLOS Genetics: published November 7, 2016 | https://doi.org/10.1371/journal.pgen.1006414

CDC-42 Orients Cell Migration during Epithelial Intercalation in the Caenorhabditis elegans Epidermis

Elise Walck-Shannon, Bethany Lucas, Ian Chin-Sang, David Reiner, Kraig Kumfer, Hunter Cochran, William Bothfeld, Jeff Hardin

PLOS Genetics: published November 18, 2016 | https://doi.org/10.1371/journal.pgen.1006415

The miR165/166 Mediated Regulatory Module Plays Critical Roles in ABA Homeostasis and Response in Arabidopsis thaliana

Jun Yan, Chunzhao Zhao, Jianping Zhou, Yu Yang, Pengcheng Wang, Xiaohong Zhu, Guiliang Tang, Ray A. Bressan, Jian-Kang Zhu

PLOS Genetics: published November 3, 2016 | https://doi.org/10.1371/journal.pgen.1006416

Distinct Prion Domain Sequences Ensure Efficient Amyloid Propagation by Promoting Chaperone Binding or Processing In Vivo

Christine R. Langlois, Fen Pei, Suzanne S. Sindi, Tricia R. Serio

PLOS Genetics: published November 4, 2016 | https://doi.org/10.1371/journal.pgen.1006417

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

Marta Lourenço, Ricardo S. Ramiro, Daniela Güleresi, João Barroso-Batista, Karina B. Xavier, Isabel Gordo, Ana Sousa

PLOS Genetics: published November 3, 2016 | https://doi.org/10.1371/journal.pgen.1006420

The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis

Wen Huang, Trudy F. C. Mackay

PLOS Genetics: published November 3, 2016 | https://doi.org/10.1371/journal.pgen.1006421

Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

Ziwei Li, Shengpeng Wang, Jinping Cheng, Chuanbin Su, Songxiao Zhong, Qi Liu, Yuda Fang, Yao Yu, Hong Lv, Yun Zheng, Binglian Zheng

PLOS Genetics: published November 21, 2016 | https://doi.org/10.1371/journal.pgen.1006422

Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues

Heather E. Wheeler, Kaanan P. Shah, Jonathon Brenner, Tzintzuni Garcia, Keston Aquino-Michaels, GTEx Consortium, Nancy J. Cox, Dan L. Nicolae, Hae Kyung Im

PLOS Genetics: published November 11, 2016 | https://doi.org/10.1371/journal.pgen.1006423

Scribbled Optimizes BMP Signaling through Its Receptor Internalization to the Rab5 Endosome and Promote Robust Epithelial Morphogenesis

Jinghua Gui, Yunxian Huang, Osamu Shimmi

PLOS Genetics: published November 4, 2016 | https://doi.org/10.1371/journal.pgen.1006424

Pleiotropic Mechanisms Indicated for Sex Differences in Autism

Ileena Mitra, Kathryn Tsang, Christine Ladd-Acosta, Lisa A. Croen, Kimberly A. Aldinger, Robert L. Hendren, Michela Traglia, Alinoë Lavillaureix, Noah Zaitlen, Michael C. Oldham, Pat Levitt, Stanley Nelson, David G. Amaral, Irva Herz-Picciotto, M. Daniele Fallin, Lauren A. Weiss

PLOS Genetics: published November 15, 2016 | https://doi.org/10.1371/journal.pgen.1006425

Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting

Marta Sanchez-Delgado, Franck Court, Enrique Vidal, Jose Medrano, Ana Monteagudo-Sánchez, Alex Martin-Trujillo, Chiharu Tayama, Isabel Iglesias-Platas, Ivanela Kondova, Ronald Bontrop, Maria Eugenia Poo-Llanillo, Tomas Marques-Bonet, Kazuhiko Nakabayashi, Carlos Simón, David Monk

PLOS Genetics: published November 11, 2016 | https://doi.org/10.1371/journal.pgen.1006427

Regional Control of Chromosome Segregation in Pseudomonas aeruginosa

Valentine Lagage, Frédéric Boccard, Isabelle Vallet-Gely

PLOS Genetics: published November 7, 2016 | https://doi.org/10.1371/journal.pgen.1006428

Proteomic Landscape of Tissue-Specific Cyclin E Functions in Vivo

Junko Odajima, Siddharth Saini, Piotr Jung, Yasmine Ndassa-Colday, Scott Ficaro, Yan Geng, Eugenio Marco, Wojciech Michowski, Yaoyu E. Wang, James A. DeCaprio, Larisa Litovchick, Jarrod Marto, Piotr Sicinski

PLOS Genetics: published November 9, 2016 | https://doi.org/10.1371/journal.pgen.1006429

CLOCKWORK ORANGE Enhances PERIOD Mediated Rhythms in Transcriptional Repression by Antagonizing E-box Binding by CLOCK-CYCLE

Jian Zhou, Wangjie Yu, Paul E. Hardin

PLOS Genetics: published November 4, 2016 | https://doi.org/10.1371/journal.pgen.1006430

Prion-Associated Toxicity is Rescued by Elimination of Cotranslational Chaperones

Kathryn M. Keefer, Heather L. True

PLOS Genetics: published November 9, 2016 | https://doi.org/10.1371/journal.pgen.1006431

MTV, an ssDNA Protecting Complex Essential for Transposon-Based Telomere Maintenance in Drosophila

Yi Zhang, Liang Zhang, Xiaona Tang, Shilpa R. Bhardwaj, Jingyun Ji, Yikang S. Rong

PLOS Genetics: published November 11, 2016 | https://doi.org/10.1371/journal.pgen.1006435

Phosphorylation of CBP20 Links MicroRNA to Root Growth in the Ethylene Response

Fan Zhang, Likai wang, Jae Yun Lim, Taewook Kim, Youngjae Pyo, Sibum Sung, Chanseok Shin, Hong Qiao

PLOS Genetics: published November 21, 2016 | https://doi.org/10.1371/journal.pgen.1006437

A Novel Zebrafish ret Heterozygous Model of Hirschsprung Disease Identifies a Functional Role for mapk10 as a Modifier of Enteric Nervous System Phenotype Severity

Tiffany A. Heanue, Werend Boesmans, Donald M. Bell, Koichi Kawakami, Pieter Vanden Berghe, Vassilis Pachnis

PLOS Genetics: published November 30, 2016 | https://doi.org/10.1371/journal.pgen.1006439

Myosin phosphatase Fine-tunes Zebrafish Motoneuron Position during Axonogenesis

Juliane Bremer, Michael Granato

PLOS Genetics: published November 17, 2016 | https://doi.org/10.1371/journal.pgen.1006440

Maintenance of Taste Organs Is Strictly Dependent on Epithelial Hedgehog/GLI Signaling

Alexandre N. Ermilov, Archana Kumari, Libo Li, Ariell M. Joiner, Marina A. Grachtchouk, Benjamin L. Allen, Andrzej A. Dlugosz, Charlotte M. Mistretta

PLOS Genetics: published November 28, 2016 | https://doi.org/10.1371/journal.pgen.1006442

Loss of C9orf72 Enhances Autophagic Activity via Deregulated mTOR and TFEB Signaling

Janet Ugolino, Yon Ju Ji, Karen Conchina, Justin Chu, Raja Sekhar Nirujogi, Akhilesh Pandey, Nathan R. Brady, Anne Hamacher-Brady, Jiou Wang

PLOS Genetics: published November 22, 2016 | https://doi.org/10.1371/journal.pgen.1006443

Genetically Blocking the Zebrafish Pineal Clock Affects Circadian Behavior

Zohar Ben-Moshe Livne, Shahar Alon, Daniela Vallone, Yared Bayleyen, Adi Tovin, Inbal Shainer, Laura G. Nisembaum, Idit Aviram, Sima Smadja-Storz, Michael Fuentes, Jack Falcón, Eli Eisenberg, David C. Klein, Harold A. Burgess, Nicholas S. Foulkes, Yoav Gothilf

PLOS Genetics: published November 21, 2016 | https://doi.org/10.1371/journal.pgen.1006445

Mechanisms for Complex Chromosomal Insertions

Shen Gu, Przemyslaw Szafranski, Zeynep Coban Akdemir, Bo Yuan, Mitchell L. Cooper, Maria A. Magriñá, Carlos A. Bacino, Seema R. Lalani, Amy M. Breman, Janice L. Smith, Ankita Patel, Rodger H. Song, Weimin Bi, Sau Wai Cheung, Claudia M. B. Carvalho, Paweł Stankiewicz, James R. Lupski

PLOS Genetics: published November 23, 2016 | https://doi.org/10.1371/journal.pgen.1006446

Genomic Characterization of Metformin Hepatic Response

Marcelo R. Luizon, Walter L. Eckalbar, Yao Wang, Stacy L. Jones, Robin P. Smith, Megan Laurance, Lawrence Lin, Paul J. Gallins, Amy S. Etheridge, Fred Wright, Yihui Zhou, Cliona Molony, Federico Innocenti, Sook Wah Yee, Kathleen M. Giacomini, Nadav Ahituv

PLOS Genetics: published November 30, 2016 | https://doi.org/10.1371/journal.pgen.1006449

Functional Genomic Analysis of Candida albicans Adherence Reveals a Key Role for the Arp2/3 Complex in Cell Wall Remodelling and Biofilm Formation

Jason A. Lee, Nicole Robbins, Jinglin L. Xie, Troy Ketela, Leah E. Cowen

PLOS Genetics: published November 21, 2016 | https://doi.org/10.1371/journal.pgen.1006452

Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton

Hao Chen, Terence D. Capellini, Michael Schoor, Doug P. Mortlock, A. Hari Reddi, David M. Kingsley

PLOS Genetics: published November 30, 2016 | https://doi.org/10.1371/journal.pgen.1006454

Neuronal Ndrg4 Is Essential for Nodes of Ranvier Organization in Zebrafish

Laura Fontenas, Flavia De Santis, Vincenzo Di Donato, Cindy Degerny, Béatrice Chambraud, Filippo Del Bene, Marcel Tawk

PLOS Genetics: published November 30, 2016 | https://doi.org/10.1371/journal.pgen.1006459

Cover

Patterning synovial joints in vertebrates.

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