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Table of Contents: September 2018

This painting summarizes the concepts underlying this work. The blood vessel in the center of the painting contains a thrombus, the phenotypic target for our screen. The left side of the painting depicts a pedigree generated from a male mouse following treatment with the chemical mutagen ENU (red formula) as well as a Sanger Sequencing trace with a representative ENU-induced variant. The right side of the painting depicts genotyping and mapping to identify the causal variant. The original acrylic painting created by Kärt Tomberg is located at the Life Sciences Institute, University of Michigan. See Tomberg et al.

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Image Credit: Kärt Tomberg, University of Michigan

Editorial

2018 PLOS Genetics Research Prize: Bundling, stabilizing, organizing—The orchestration of acentriolar spindle assembly by microtubule motor proteins

Gregory S. Barsh, Needhi Bhalla, Francesca Cole, Gregory P. Copenhaver, Soni Lacefield, Diana E. Libuda

Review

Structure and function of archaeal histones

Bram Henneman, Clara van Emmerik, Hugo van Ingen, Remus T. Dame

Research Articles

Epistatic control of intrinsic resistance by virulence genes in Listeria

Mariela Scortti, Lei Han, Sonsiray Alvarez, Alexandre Leclercq, Alexandra Moura, Marc Lecuit, Jose Vazquez-Boland

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Dynamic SUMO remodeling drives a series of critical events during the meiotic divisions in Caenorhabditis elegans

Amanda C. Davis-Roca, Nikita S. Divekar, Rachel K. Ng, Sarah M. Wignall

Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis

William P. D. Hendricks, Victoria Zismann, Karthigayini Sivaprakasam, Christophe Legendre, Kelsey Poorman, Waibhav Tembe, Nieves Perdigones, Jeffrey Kiefer, Winnie Liang, Valerie DeLuca, Mitchell Stark, Alison Ruhe, Roe Froman, Nicholas S. Duesbery, Megan Washington, Jessica Aldrich, Mark W. Neff, Matthew J. Huentelman, Nicholas Hayward, Kevin Brown, Douglas Thamm, Gerald Post, Chand Khanna, Barbara Davis, Matthew Breen, Alexander Sekulic, Jeffrey M. Trent

The conserved protective cyclic AMP-phosphodiesterase function PDE4B is expressed in the adenoma and adjacent normal colonic epithelium of mammals and silenced in colorectal cancer

Jennifer K. Pleiman, Amy A. Irving, Zhishi Wang, Erik Toraason, Linda Clipson, William F. Dove, Dustin A. Deming, Michael A. Newton

Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal

Choongwon Jeong, David B. Witonsky, Buddha Basnyat, Maniraj Neupane, Cynthia M. Beall, Geoff Childs, Sienna R. Craig, John Novembre, Anna Di Rienzo

Whole exome sequencing of ENU-induced thrombosis modifier mutations in the mouse

Kärt Tomberg, Randal J. Westrick, Emilee N. Kotnik, Audrey C. Cleuren, David R Siemieniak, Guojing Zhu, Thomas L. Saunders, David Ginsburg

FGF-induced Pea3 transcription factors program the genetic landscape for cell fate determination

Ankur Garg, Abdul Hannan, Qian Wang, Tamica Collins, Siying Teng, Mukesh Bansal, Jian Zhong, Keli Xu, Xin Zhang

In search of the Goldilocks zone for hybrid speciation

Alexandre Blanckaert, Claudia Bank

Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos

Ben J. Vincent, Max V. Staller, Francheska Lopez-Rivera, Meghan D. J. Bragdon, Edward C. G. Pym, Kelly M. Biette, Zeba Wunderlich, Timothy T. Harden, Javier Estrada, Angela H. DePace

Reduced monocyte and macrophage TNFSF15/TL1A expression is associated with susceptibility to inflammatory bowel disease

Arianne C. Richard, James E. Peters, Natalia Savinykh, James C. Lee, Eric T. Hawley, Françoise Meylan, Richard M. Siegel, Paul A. Lyons, Kenneth G. C. Smith

MiR-202 controls female fecundity by regulating medaka oogenesis

Stéphanie Gay, Jérôme Bugeon, Amine Bouchareb, Laure Henry, Clara Delahaye, Fabrice Legeai, Jérôme Montfort, Aurélie Le Cam, Anne Siegel, Julien Bobe, Violette Thermes

Physiological and pathological roles of FATP-mediated lipid droplets in Drosophila and mice retina

Daan M. Van Den Brink, Aurélie Cubizolle, Gilles Chatelain, Nathalie Davoust, Victor Girard, Simone Johansen, Francesco Napoletano, Pierre Dourlen, Laurent Guillou, Claire Angebault-Prouteau, Nathalie Bernoud-Hubac, Michel Guichardant, Philippe Brabet, Bertrand Mollereau

Transcription factor CBF-1 is critical for circadian gene expression by modulating WHITE COLLAR complex recruitment to the frq locus

Xuemei Cao, Xiao Liu, Hongda Li, Yumeng Fan, Jiabin Duan, Yi Liu, Qun He

Robust activation of microhomology-mediated end joining for precision gene editing applications

Hirotaka Ata, Thomas L. Ekstrom, Gabriel Martínez-Gálvez, Carla M. Mann, Alexey V. Dvornikov, Kyle J. Schaefbauer, Alvin C. Ma, Drena Dobbs, Karl J. Clark, Stephen C. Ekker

Flexibility and constraint: Evolutionary remodeling of the sporulation initiation pathway in Firmicutes

Philip Davidson, Rory Eutsey, Brendan Redler, N. Luisa Hiller, Michael T. Laub, Dannie Durand

Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability

Franck Raynaud, Marco Mina, Daniele Tavernari, Giovanni Ciriello

Activating PAX gene family paralogs to complement PAX5 leukemia driver mutations

Matthew R. Hart, Donovan J. Anderson, Christopher C. Porter, Tobias Neff, Michael Levin, Marshall S. Horwitz

MAPK and GSK3/ß-TRCP-mediated degradation of the maternal Ets domain transcriptional repressor Yan/Tel controls the spatial expression of nodal in the sea urchin embryo

M. Dolores Molina, Magali Quirin, Emmanuel Haillot, Noémie De Crozé, Ryan Range, Mathieu Rouel, Felipe Jimenez, Radja Amrouche, Aline Chessel, Thierry Lepage

Disrupted structure and aberrant function of CHIP mediates the loss of motor and cognitive function in preclinical models of SCAR16

Chang-he Shi, Carrie Rubel, Sarah E. Soss, Rebekah Sanchez-Hodge, Shuo Zhang, Sabrina C. Madrigal, Saranya Ravi, Holly McDonough, Richard C. Page, Walter J. Chazin, Cam Patterson, Cheng-yuan Mao, Monte S. Willis, Hai-Yang Luo, Yu-sheng Li, Donte A. Stevens, Mi-bo Tang, Pan Du, Yao-he Wang, Zheng-wei Hu, Yu-ming Xu, Jonathan C. Schisler

Topoisomerases I and III inhibit R-loop formation to prevent unregulated replication in the chromosomal Ter region of Escherichia coli

Julien Brochu, Émilie Vlachos-Breton, Sarah Sutherland, Makisha Martel, Marc Drolet

The topoisomerase 3α zinc-finger domain T1 of Arabidopsis thaliana is required for targeting the enzyme activity to Holliday junction-like DNA repair intermediates

Annika Dorn, Sarah Röhrig, Kristin Papp, Susan Schröpfer, Frank Hartung, Alexander Knoll, Holger Puchta

Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes

Jessica E. Spiewak, Emily J. Bain, Jin Liu, Kellie Kou, Samantha L. Sturiale, Larissa B. Patterson, Parham Diba, Judith S. Eisen, Ingo Braasch, Julia Ganz, David M. Parichy

Detecting archaic introgression using an unadmixed outgroup

Laurits Skov, Ruoyun Hui, Vladimir Shchur, Asger Hobolth, Aylwyn Scally, Mikkel Heide Schierup, Richard Durbin

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome

Martijn F. L. Derks, Marcos S. Lopes, Mirte Bosse, Ole Madsen, Bert Dibbits, Barbara Harlizius, Martien A. M. Groenen, Hendrik-Jan Megens

Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene

Wangsheng Zhu, Maricris Zaidem, Anna-Lena Van de Weyer, Rafal M. Gutaker, Eunyoung Chae, Sang-Tae Kim, Felix Bemm, Lei Li, Marco Todesco, Rebecca Schwab, Frederik Unger, Marcel Janis Beha, Monika Demar, Detlef Weigel

Genome-wide association studies and CRISPR/Cas9-mediated gene editing identify regulatory variants influencing eyebrow thickness in humans

Sijie Wu, Manfei Zhang, Xinzhou Yang, Fuduan Peng, Juan Zhang, Jingze Tan, Yajun Yang, Lina Wang, Yanan Hu, Qianqian Peng, Jinxi Li, Yu Liu, Yaqun Guan, Chen Chen, Merel A. Hamer, Tamar Nijsten, Changqing Zeng, Kaustubh Adhikari, Carla Gallo, Giovanni Poletti, Lavinia Schuler-Faccini, Maria-Cátira Bortolini, Samuel Canizales-Quinteros, Francisco Rothhammer, Gabriel Bedoya, Rolando González-José, Hui Li, Jean Krutmann, Fan Liu, Manfred Kayser, Andres Ruiz-Linares, Kun Tang, Shuhua Xu, Liang Zhang, Li Jin, Sijia Wang

Hrg1 promotes heme-iron recycling during hemolysis in the zebrafish kidney

Jianbing Zhang, Ian Chambers, Sijung Yun, John Phillips, Michael Krause, Iqbal Hamza

The genomic basis of environmental adaptation in house mice

Megan Phifer-Rixey, Ke Bi, Kathleen G. Ferris, Michael J. Sheehan, Dana Lin, Katya L. Mack, Sara M. Keeble, Taichi A. Suzuki, Jeffrey M. Good, Michael W. Nachman

Formation of phenotypic lineages in Salmonella enterica by a pleiotropic fimbrial switch

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Genetic basis of thermal plasticity variation in Drosophila melanogaster body size

Elvira Lafuente, David Duneau, Patrícia Beldade

Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles

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Dissection of Nidogen function in Drosophila reveals tissue-specific mechanisms of basement membrane assembly

Jianli Dai, Beatriz Estrada, Sofie Jacobs, Besaiz J. Sánchez-Sánchez, Jia Tang, Mengqi Ma, Patricia Magadán-Corpas, José C. Pastor-Pareja, María D. Martín-Bermudo

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Rer1-mediated quality control system is required for neural stem cell maintenance during cerebral cortex development

Taichi Hara, Ikuko Maejima, Tomoko Akuzawa, Rika Hirai, Hisae Kobayashi, Satoshi Tsukamoto, Mika Tsunoda, Aguri Ono, Shota Yamakoshi, Satoshi Oikawa, Ken Sato

Tankyrases maintain homeostasis of intestinal epithelium by preventing cell death

Pan Ye, Y. Jeffrey Chiang, Zhen Qi, Yehua Li, Shan Wang, Yuan Liu, Xintong Li, Ye-Guang Chen

Mutation load dynamics during environmentally-driven range shifts

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Positive and negative regulation of transferred nif genes mediated by indigenous GlnR in Gram-positive Paenibacillus polymyxa

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Components of Brachypodium distachyon resistance to nonadapted wheat stripe rust pathogens are simply inherited

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The genetic architecture of colonization resistance in Brachypodium distachyon to non-adapted stripe rust (Puccinia striiformis) isolates

Jan Bettgenhaeuser, Matthew Gardiner, Rebecca Spanner, Phon Green, Inmaculada Hernández-Pinzón, Amelia Hubbard, Michael Ayliffe, Matthew J. Moscou

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Correction

Correction: Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth

Johanna M. Huusko, Minna K. Karjalainen, Britney E. Graham, Ge Zhang, Emily G. Farrow, Neil A. Miller, Bo Jacobsson, Haley R. Eidem, Jeffrey C. Murray, Bruce Bedell, Patrick Breheny, Noah W. Brown, Frans L. Bødker, Nadia K. Litterman, Pan-Pan Jiang, Laura Russell, David A. Hinds, Youna Hu, the 23andMe Research Team, Antonis Rokas, Kari Teramo, Kaare Christensen, Scott M. Williams, Mika Rämet, Stephen F. Kingsmore, Kelli K. Ryckman, Mikko Hallman, Louis J. Muglia

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