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Table of Contents

January 2019

Cover

DNA repair during meiosis and chromosomal bridges.
Issue Image

Meiotic cells respond to DNA damage triggering diverse repair mechanisms in a cell cycle-dependent manner. Sequential activation of these mechanisms contribute to accurately maintain genome integrity. However, when spermatocytes are exposed to exogenous DNA damaging agents, like gamma radiation, repair homeostasis may be stressed and chromosomes sometimes engage in aberrant connections with non-homologous chromosomes. Super-resolution fluorescence image (STED) of two meiotic bivalents labelled with an antibody against the SYCP3 protein of the synaptonemal complex. Parallel lines represent the trajectory of homologous chromosomes within each bivalent. A protein filament bridges from one bivalent to the other, connecting two non-homologous chromosomes. See Enguita-Marruedo et al.

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Image Credit: Marta Martín-Ruiz

Viewpoints

Wagging the long tail of drivers of prostate cancer

Vincent L. Cannataro, Jeffrey P. Townsend

PLOS Genetics: published January 17, 2019 | https://doi.org/10.1371/journal.pgen.1007820

An interaction-based model for neuropsychiatric features of copy-number variants

Matthew Jensen, Santhosh Girirajan

PLOS Genetics: published January 17, 2019 | https://doi.org/10.1371/journal.pgen.1007879

Perspective

It starts at the ends: The zebrafish meiotic bouquet is where it all begins

Kellee R. Siegfried

PLOS Genetics: published January 17, 2019 | https://doi.org/10.1371/journal.pgen.1007854

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Research Articles

Conserved function of the matriptase-prostasin proteolytic cascade during epithelial morphogenesis

Leonard Drees, Tatiana Königsmann, Martin H. J. Jaspers, Ralf Pflanz, Dietmar Riedel, Reinhard Schuh

PLOS Genetics: published January 2, 2019 | https://doi.org/10.1371/journal.pgen.1007882

RNase H1 directs origin-specific initiation of DNA replication in human mitochondria

Viktor Posse, Ali Al-Behadili, Jay P. Uhler, Anders R. Clausen, Aurelio Reyes, Massimo Zeviani, Maria Falkenberg, Claes M. Gustafsson

PLOS Genetics: published January 3, 2019 | https://doi.org/10.1371/journal.pgen.1007781

Meiosis-specific prophase-like pathway controls cleavage-independent release of cohesin by Wapl phosphorylation

Kiran Challa, Ghanim Fajish V, Miki Shinohara, Franz Klein, Susan M. Gasser, Akira Shinohara

PLOS Genetics: published January 3, 2019 | https://doi.org/10.1371/journal.pgen.1007851

LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus

Takuya Suzaki, Naoya Takeda, Hanna Nishida, Motomi Hoshino, Momoyo Ito, Fumika Misawa, Yoshihiro Handa, Kenji Miura, Masayoshi Kawaguchi

PLOS Genetics: published January 3, 2019 | https://doi.org/10.1371/journal.pgen.1007865

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  1. Correction: LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus

The effector of Hippo signaling, Taz, is required for formation of the micropyle and fertilization in zebrafish

Xiaogui Yi, Jia Yu, Chao Ma, Guoping Dong, Wenpeng Shi, Hongtao Li, Li Li, Lingfei Luo, Karuna Sampath, Hua Ruan, Honghui Huang

PLOS Genetics: published January 4, 2019 | https://doi.org/10.1371/journal.pgen.1007408

Hormonal signaling cascades required for phototaxis switch in wandering Leptinotarsa decemlineata larvae

Qing-Wei Meng, Qing-Yu Xu, Tao-Tao Zhu, Lin Jin, Kai-Yun Fu, Wen-Chao Guo, Guo-Qing Li

PLOS Genetics: published January 7, 2019 | https://doi.org/10.1371/journal.pgen.1007423

A cation diffusion facilitator, GmCDF1, negatively regulates salt tolerance in soybean

Wei Zhang, Xiliang Liao, Yanmei Cui, Weiyu Ma, Xinnan Zhang, Hongyang Du, Yujie Ma, Lihua Ning, Hui Wang, Fang Huang, Hui Yang, Guizhen Kan, Deyue Yu

PLOS Genetics: published January 7, 2019 | https://doi.org/10.1371/journal.pgen.1007798

CDI/CDS system-encoding genes of Burkholderia thailandensis are located in a mobile genetic element that defines a new class of transposon

Angelica B. Ocasio, Peggy A. Cotter

PLOS Genetics: published January 7, 2019 | https://doi.org/10.1371/journal.pgen.1007883

Narya, a RING finger domain-containing protein, is required for meiotic DNA double-strand break formation and crossover maturation in Drosophila melanogaster

Cathleen M. Lake, Rachel J. Nielsen, Amanda M. Bonner, Salam Eche, Sanese White-Brown, Kim S. McKim, R. Scott Hawley

PLOS Genetics: published January 7, 2019 | https://doi.org/10.1371/journal.pgen.1007886

Functional divergence of a global regulatory complex governing fungal filamentation

Elizabeth J. Polvi, Amanda O. Veri, Zhongle Liu, Saif Hossain, Sabrina Hyde, Sang Hu Kim, Faiza Tebbji, Adnane Sellam, Robert T. Todd, Jinglin L. Xie, Zhen-Yuan Lin, Cassandra J. Wong, Rebecca S. Shapiro, Malcolm Whiteway, Nicole Robbins, Anne-Claude Gingras, Anna Selmecki, Leah E. Cowen

PLOS Genetics: published January 7, 2019 | https://doi.org/10.1371/journal.pgen.1007901

BRASSINOSTEROID-SIGNALING KINASE 3, a plasma membrane-associated scaffold protein involved in early brassinosteroid signaling

Hong Ren, Björn C. Willige, Yvon Jaillais, Sa Geng, Mee Yeon Park, William M. Gray, Joanne Chory

PLOS Genetics: published January 7, 2019 | https://doi.org/10.1371/journal.pgen.1007904

Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting

Orsolya Symmons, Marcello Chang, Ian A. Mellis, Jennifer M. Kalish, Jihwan Park, Katalin Suszták, Marisa S. Bartolomei, Arjun Raj

PLOS Genetics: published January 9, 2019 | https://doi.org/10.1371/journal.pgen.1007874

Plasma membrane architecture protects Candida albicans from killing by copper

Lois M. Douglas, James B. Konopka

PLOS Genetics: published January 11, 2019 | https://doi.org/10.1371/journal.pgen.1007911

Diapause induces functional axonal regeneration after necrotic insult in C. elegans

Mauricio Caneo, Victoria Julian, Alexandra B. Byrne, Mark J. Alkema, Andrea Calixto

PLOS Genetics: published January 14, 2019 | https://doi.org/10.1371/journal.pgen.1007863

CDK contribution to DSB formation and recombination in fission yeast meiosis

Luisa F. Bustamante-Jaramillo, Celia Ramos, Leticia Alonso, Aroa Sesmero, Mónica Segurado, Cristina Martín-Castellanos

PLOS Genetics: published January 14, 2019 | https://doi.org/10.1371/journal.pgen.1007876

Estimating recent migration and population-size surfaces

Hussein Al-Asadi, Desislava Petkova, Matthew Stephens, John Novembre

PLOS Genetics: published January 14, 2019 | https://doi.org/10.1371/journal.pgen.1007908

The apical protein Apnoia interacts with Crumbs to regulate tracheal growth and inflation

Kassiani Skouloudaki, Dimitrios K. Papadopoulos, Pavel Tomancak, Elisabeth Knust

PLOS Genetics: published January 15, 2019 | https://doi.org/10.1371/journal.pgen.1007852

The telomere bouquet is a hub where meiotic double-strand breaks, synapsis, and stable homolog juxtaposition are coordinated in the zebrafish, Danio rerio

Yana P. Blokhina, An D. Nguyen, Bruce W. Draper, Sean M. Burgess

PLOS Genetics: published January 17, 2019 | https://doi.org/10.1371/journal.pgen.1007730

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Admixture mapping reveals evidence of differential multiple sclerosis risk by genetic ancestry

Calvin Chi, Xiaorong Shao, Brooke Rhead, Edlin Gonzales, Jessica B. Smith, Anny H. Xiang, Jennifer Graves, Amy Waldman, Timothy Lotze, Teri Schreiner, Bianca Weinstock-Guttman, Gregory Aaen, Jan-Mendelt Tillema, Jayne Ness, Meghan Candee, Lauren Krupp, Mark Gorman, Leslie Benson, Tanuja Chitnis, Soe Mar, Anita Belman, Theron Charles Casper, John Rose, Manikum Moodley, Mary Rensel, Moses Rodriguez, Benjamin Greenberg, Llana Kahn, Jennifer Rubin, Catherine Schaefer, Emmanuelle Waubant, Annette Langer-Gould, Lisa F. Barcellos

PLOS Genetics: published January 17, 2019 | https://doi.org/10.1371/journal.pgen.1007808

Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation

Andrea Callegari, Christian Sieben, Alexander Benke, David M. Suter, Beat Fierz, Davide Mazza, Suliana Manley

PLOS Genetics: published January 17, 2019 | https://doi.org/10.1371/journal.pgen.1007891

The complex architecture and epigenomic impact of plant T-DNA insertions

Florian Jupe, Angeline C. Rivkin, Todd P. Michael, Mark Zander, S. Timothy Motley, Justin P. Sandoval, R. Keith Slotkin, Huaming Chen, Rosa Castanon, Joseph R. Nery, Joseph R. Ecker

PLOS Genetics: published January 18, 2019 | https://doi.org/10.1371/journal.pgen.1007819

SUMO modification of LBD30 by SIZ1 regulates secondary cell wall formation in Arabidopsis thaliana

Chang Liu, Hasi Yu, Laigeng Li

PLOS Genetics: published January 18, 2019 | https://doi.org/10.1371/journal.pgen.1007928

Transition from a meiotic to a somatic-like DNA damage response during the pachytene stage in mouse meiosis

Andrea Enguita-Marruedo, Marta Martín-Ruiz, Eva García, Ana Gil-Fernández, María Teresa Parra, Alberto Viera, Julio S. Rufas, Jesús Page

PLOS Genetics: published January 22, 2019 | https://doi.org/10.1371/journal.pgen.1007439

Artificial selection on storage protein 1 possibly contributes to increase of hatchability during silkworm domestication

Ya-Nan Zhu, Li-Zhi Wang, Cen-Cen Li, Yong Cui, Man Wang, Yong-Jian Lin, Ruo-Ping Zhao, Wen Wang, Hui Xiang

PLOS Genetics: published January 22, 2019 | https://doi.org/10.1371/journal.pgen.1007616

Integrating predicted transcriptome from multiple tissues improves association detection

Alvaro N. Barbeira, Milton Pividori, Jiamao Zheng, Heather E. Wheeler, Dan L. Nicolae, Hae Kyung Im

PLOS Genetics: published January 22, 2019 | https://doi.org/10.1371/journal.pgen.1007889

Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer

Marion Faucher, Laurent-Xavier Nouvel, Emilie Dordet-Frisoni, Eveline Sagné, Eric Baranowski, Marie-Claude Hygonenq, Marc-Serge Marenda, Florence Tardy, Christine Citti

PLOS Genetics: published January 22, 2019 | https://doi.org/10.1371/journal.pgen.1007910

The nuclear hormone receptor NHR-86 controls anti-pathogen responses in C. elegans

Nicholas D. Peterson, Hilary K. Cheesman, Pengpeng Liu, Sarah M. Anderson, Kyle J. Foster, Richa Chhaya, Paola Perrat, Jose Thekkiniath, Qiyuan Yang, Cole M. Haynes, Read Pukkila-Worley

PLOS Genetics: published January 22, 2019 | https://doi.org/10.1371/journal.pgen.1007935

Genetic architecture of human thinness compared to severe obesity

Fernando Riveros-McKay, Vanisha Mistry, Rebecca Bounds, Audrey Hendricks, Julia M. Keogh, Hannah Thomas, Elana Henning, Laura J. Corbin, Understanding Society Scientific Group, Stephen O’Rahilly, Eleftheria Zeggini, Eleanor Wheeler, Inês Barroso, I. Sadaf Farooqi

PLOS Genetics: published January 24, 2019 | https://doi.org/10.1371/journal.pgen.1007603

Serotonin and neuropeptides are both released by the HSN command neuron to initiate Caenorhabditis elegans egg laying

Jacob C. Brewer, Andrew C. Olson, Kevin M. Collins, Michael R. Koelle

PLOS Genetics: published January 24, 2019 | https://doi.org/10.1371/journal.pgen.1007896

Intronic CNVs and gene expression variation in human populations

Maria Rigau, David Juan, Alfonso Valencia, Daniel Rico

PLOS Genetics: published January 24, 2019 | https://doi.org/10.1371/journal.pgen.1007902

Dissecting the pathways coordinating patterning and growth by plant boundary domains

Aude Maugarny-Calès, Millán Cortizo, Bernard Adroher, Nero Borrega, Beatriz Gonçalves, Geraldine Brunoud, Teva Vernoux, Nicolas Arnaud, Patrick Laufs

PLOS Genetics: published January 24, 2019 | https://doi.org/10.1371/journal.pgen.1007913

Ask1 and Akt act synergistically to promote ROS-dependent regeneration in Drosophila

Paula Santabárbara-Ruiz, José Esteban-Collado, Lidia Pérez, Giacomo Viola, Josep F. Abril, Marco Milán, Montserrat Corominas, Florenci Serras

PLOS Genetics: published January 24, 2019 | https://doi.org/10.1371/journal.pgen.1007926

RPGRIP1L is required for stabilizing epidermal keratinocyte adhesion through regulating desmoglein endocytosis

Yeon Ja Choi, Christine Laclef, Ning Yang, Abraham Andreu-Cervera, Joshua Lewis, Xuming Mao, Li Li, Elizabeth R. Snedecor, Ken-Ichi Takemaru, Chuan Qin, Sylvie Schneider-Maunoury, Kenneth R. Shroyer, Yusuf A. Hannun, Peter J. Koch, Richard A. Clark, Aimee S. Payne, Andrew P. Kowalczyk, Jiang Chen

PLOS Genetics: published January 28, 2019 | https://doi.org/10.1371/journal.pgen.1007914

TCTP and CSN4 control cell cycle progression and development by regulating CULLIN1 neddylation in plants and animals

Léo Betsch, Véronique Boltz, Florian Brioudes, Garance Pontier, Victor Girard, Julie Savarin, Barbara Wipperman, Pierre Chambrier, Nicolas Tissot, Moussa Benhamed, Bertrand Mollereau, Cécile Raynaud, Mohammed Bendahmane, Judit Szécsi

PLOS Genetics: published January 29, 2019 | https://doi.org/10.1371/journal.pgen.1007899

Regeneration of the zebrafish retinal pigment epithelium after widespread genetic ablation

Nicholas J. Hanovice, Lyndsay L. Leach, Kayleigh Slater, Ana E. Gabriel, Dwight Romanovicz, Enhua Shao, Ross Collery, Edward A. Burton, Kira L. Lathrop, Brian A. Link, Jeffrey M. Gross

PLOS Genetics: published January 29, 2019 | https://doi.org/10.1371/journal.pgen.1007939

Heme peroxidase HPX-2 protects Caenorhabditis elegans from pathogens

Yi Liu, Karan Gautam Kaval, Ambro van Hoof, Danielle A. Garsin

PLOS Genetics: published January 29, 2019 | https://doi.org/10.1371/journal.pgen.1007944

Balancing selection at a premature stop mutation in the myostatin gene underlies a recessive leg weakness syndrome in pigs

Oswald Matika, Diego Robledo, Ricardo Pong-Wong, Stephen C. Bishop, Valentina Riggio, Heather Finlayson, Natalie R. Lowe, Annabelle E. Hoste, Grant A. Walling, Jorge del-Pozo, Alan L. Archibald, John A. Woolliams, Ross D. Houston

PLOS Genetics: published January 30, 2019 | https://doi.org/10.1371/journal.pgen.1007759

Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation

Mary Leatham-Jensen, Christopher M. Uyehara, Brian D. Strahl, A. Gregory Matera, Robert J. Duronio, Daniel J. McKay

PLOS Genetics: published January 30, 2019 | https://doi.org/10.1371/journal.pgen.1007932

Early girl is a novel component of the Fat signaling pathway

Jyoti R. Misra, Kenneth D. Irvine

PLOS Genetics: published January 30, 2019 | https://doi.org/10.1371/journal.pgen.1007955

Exposure of Candida albicans β (1,3)-glucan is promoted by activation of the Cek1 pathway

Tian Chen, Joseph W. Jackson, Robert N. Tams, Sarah E. Davis, Timothy E. Sparer, Todd B. Reynolds

PLOS Genetics: published January 31, 2019 | https://doi.org/10.1371/journal.pgen.1007892

O-GlcNAcylation of PERIOD regulates its interaction with CLOCK and timing of circadian transcriptional repression

Ying H. Li, Xianhui Liu, Jens T. Vanselow, Haiyan Zheng, Andreas Schlosser, Joanna C. Chiu

PLOS Genetics: published January 31, 2019 | https://doi.org/10.1371/journal.pgen.1007953

Corrections

Correction: Human demographic history has amplified the effects of background selection across the genome

Raul Torres, Zachary A. Szpiech, Ryan D. Hernandez

PLOS Genetics: published January 2, 2019 | https://doi.org/10.1371/journal.pgen.1007898

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Correction: Multilevel effects of light on ribosome dynamics in chloroplasts program genome-wide and psbA-specific changes in translation

Prakitchai Chotewutmontri, Alice Barkan

PLOS Genetics: published January 3, 2019 | https://doi.org/10.1371/journal.pgen.1007907

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  1. Multilevel effects of light on ribosome dynamics in chloroplasts program genome-wide and psbA-specific changes in translation

Correction: Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs

Jonas Donner, Heidi Anderson, Stephen Davison, Angela M. Hughes, Julia Bouirmane, Johan Lindqvist, Katherine M. Lytle, Balasubramanian Ganesan, Claudia Ottka, Päivi Ruotanen, Maria Kaukonen, Oliver P. Forman, Neale Fretwell, Cynthia A. Cole, Hannes Lohi

PLOS Genetics: published January 18, 2019 | https://doi.org/10.1371/journal.pgen.1007938

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Correction: LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus

Takuya Suzaki, Naoya Takeda, Hanna Nishida, Motomi Hoshino, Momoyo Ito, Fumika Misawa, Yoshihiro Handa, Kenji Miura, Masayoshi Kawaguchi

PLOS Genetics: published January 31, 2019 | https://doi.org/10.1371/journal.pgen.1007966

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Correction: Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish

Anna M. Sokol, Barbara Uszczynska-Ratajczak, Michelle M. Collins, Michal Bazala, Ulrike Topf, Pia R. Lundegaard, Sreedevi Sugunan, Stefan Guenther, Carsten Kuenne, Johannes Graumann, Sherine S. L. Chan, Didier Y. R. Stainier, Agnieszka Chacinska

PLOS Genetics: published January 31, 2019 | https://doi.org/10.1371/journal.pgen.1007972

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