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Table of Contents

December 2018

Cover

A French Bulldog, one of the three dog breeds characterized by truncated and malformed caudal vertebrae or "screw tail".
Issue Image

Screw tail dog breeds include the Bulldog, French Bulldog and Boston terrier. These breeds share morphological characteristics including vertebral malformations, short stature, brachycephaly and widely set eyes. Breed defining characteristics for screw tail dog breeds were investigated using whole genome association analysis of all variants identified in 100 dogs (12.4 million variants). The single most associated variant was a protein truncating DVL2 frameshift variant analogous to frameshift mutations in human DVL1 and DVL3 which are responsible for Robinow syndrome. See Mansour et al.

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Image Credit: Katy Robertson

Editorial

Doubling down on forensic twin studies

Gregory P. Copenhaver, Bruce Weir, Mark Rothstein, Hua Tang, Scott M. Williams, Gregory S. Barsh

PLOS Genetics: published December 20, 2018 | https://doi.org/10.1371/journal.pgen.1007831

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Viewpoints

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2

Melissa S. Cline, Rachel G. Liao, Michael T. Parsons, Benedict Paten, Faisal Alquaddoomi, Antonis Antoniou, Samantha Baxter, Larry Brody, Robert Cook-Deegan, Amy Coffin, Fergus J. Couch, Brian Craft, Robert Currie, Chloe C. Dlott, Lena Dolman, Johan T. den Dunnen, Stephanie O. M. Dyke, Susan M. Domchek, Douglas Easton, Zachary Fischmann, William D. Foulkes, Judy Garber, David Goldgar, Mary J. Goldman, Peter Goodhand, Steven Harrison, David Haussler, Kazuto Kato, Bartha Knoppers, Charles Markello, Robert Nussbaum, Kenneth Offit, Sharon E. Plon, Jem Rashbass, Heidi L. Rehm, Mark Robson, Wendy S. Rubinstein, Dominique Stoppa-Lyonnet, Sean Tavtigian, Adrian Thorogood, Can Zhang, Marc Zimmermann, BRCA Challenge Authors, John Burn, Stephen Chanock, Gunnar Rätsch, Amanda B. Spurdle

PLOS Genetics: published December 26, 2018 | https://doi.org/10.1371/journal.pgen.1007752

Perspective

R-loops modulate Trypanosome antigenic variation

Lauren L. Prister, H. Steven Seifert

PLOS Genetics: published December 13, 2018 | https://doi.org/10.1371/journal.pgen.1007809

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Review

Population structure in genetic studies: Confounding factors and mixed models

Jae Hoon Sul, Lana S. Martin, Eleazar Eskin

PLOS Genetics: published December 27, 2018 | https://doi.org/10.1371/journal.pgen.1007309

Research Articles

Amino acid residues in five separate HLA genes can explain most of the known associations between the MHC and primary biliary cholangitis

Rebecca Darlay, Kristin L. Ayers, George F. Mells, Lynsey S. Hall, Jimmy Z. Liu, Mohamed A. Almarri, Graeme J. Alexander, David E. Jones, Richard N. Sandford, Carl A. Anderson, Heather J. Cordell

PLOS Genetics: published December 3, 2018 | https://doi.org/10.1371/journal.pgen.1007833

Ancestral origin of ApoE ε4 Alzheimer disease risk in Puerto Rican and African American populations

Farid Rajabli, Briseida E. Feliciano, Katrina Celis, Kara L. Hamilton-Nelson, Patrice L. Whitehead, Larry D. Adams, Parker L. Bussies, Clara P. Manrique, Alejandra Rodriguez, Vanessa Rodriguez, Takiyah Starks, Grace E. Byfield, Carolina B. Sierra Lopez, Jacob L. McCauley, Heriberto Acosta, Angel Chinea, Brian W. Kunkle, Christiane Reitz, Lindsay A. Farrer, Gerard D. Schellenberg, Badri N. Vardarajan, Jeffery M. Vance, Michael L. Cuccaro, Eden R. Martin, Jonathan L. Haines, Goldie S. Byrd, Gary W. Beecham, Margaret A. Pericak-Vance

PLOS Genetics: published December 5, 2018 | https://doi.org/10.1371/journal.pgen.1007791

Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 which contributes to Robinow-like syndrome in Bulldogs and related screw tail dog breeds

Tamer A. Mansour, Katherine Lucot, Sara E. Konopelski, Peter J. Dickinson, Beverly K. Sturges, Karen L. Vernau, Shannon Choi, Joshua A. Stern, Sara M. Thomasy, Sophie Döring, Frank J. M. Verstraete, Eric G. Johnson, Daniel York, Robert B. Rebhun, Hsin-Yi Henry Ho, C. Titus Brown, Danika L. Bannasch

PLOS Genetics: published December 6, 2018 | https://doi.org/10.1371/journal.pgen.1007850

Conserved mRNA-granule component Scd6 targets Dhh1 to repress translation initiation and activates Dcp2-mediated mRNA decay in vivo

Quira Zeidan, Feng He, Fan Zhang, Hongen Zhang, Allan Jacobson, Alan G. Hinnebusch

PLOS Genetics: published December 7, 2018 | https://doi.org/10.1371/journal.pgen.1007806

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The planar cell polarity protein VANG-1/Vangl negatively regulates Wnt/β-catenin signaling through a Dvl dependent mechanism

Remco A. Mentink, Lorenzo Rella, Tomasz W. Radaszkiewicz, Tomáš Gybel, Marco C. Betist, Vitězslav Bryja, Hendrik C. Korswagen

PLOS Genetics: published December 7, 2018 | https://doi.org/10.1371/journal.pgen.1007840

De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders

Hongjian Qi, Lan Yu, Xueya Zhou, Julia Wynn, Haoquan Zhao, Yicheng Guo, Na Zhu, Alexander Kitaygorodsky, Rebecca Hernan, Gudrun Aspelund, Foong-Yen Lim, Timothy Crombleholme, Robert Cusick, Kenneth Azarow, Melissa E. Danko, Dai Chung, Brad W. Warner, George B. Mychaliska, Douglas Potoka, Amy J. Wagner, Mahmoud ElFiky, Jay M. Wilson, Debbie Nickerson, Michael Bamshad, Frances A. High, Mauro Longoni, Patricia K. Donahoe, Wendy K. Chung, Yufeng Shen

PLOS Genetics: published December 10, 2018 | https://doi.org/10.1371/journal.pgen.1007822

RNA-on-X 1 and 2 in Drosophila melanogaster fulfill separate functions in dosage compensation

Maria Kim, Marie-Line Faucillion, Jan Larsson

PLOS Genetics: published December 10, 2018 | https://doi.org/10.1371/journal.pgen.1007842

Spinocerebellar ataxia type 11-associated alleles of Ttbk2 dominantly interfere with ciliogenesis and cilium stability

Emily Bowie, Ryan Norris, Kathryn V. Anderson, Sarah C. Goetz

PLOS Genetics: published December 10, 2018 | https://doi.org/10.1371/journal.pgen.1007844

Boundaries mediate long-distance interactions between enhancers and promoters in the Drosophila Bithorax complex

Nikolay Postika, Mario Metzler, Markus Affolter, Martin Müller, Paul Schedl, Pavel Georgiev, Olga Kyrchanova

PLOS Genetics: published December 12, 2018 | https://doi.org/10.1371/journal.pgen.1007702

Multiplexed CRISPR/Cas9-mediated knockout of 19 Fanconi anemia pathway genes in zebrafish revealed their roles in growth, sexual development and fertility

Ramanagouda Ramanagoudr-Bhojappa, Blake Carrington, Mukundhan Ramaswami, Kevin Bishop, Gabrielle M. Robbins, MaryPat Jones, Ursula Harper, Stephen C. Frederickson, Danielle C. Kimble, Raman Sood, Settara C. Chandrasekharappa

PLOS Genetics: published December 12, 2018 | https://doi.org/10.1371/journal.pgen.1007821

Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion

Emma Briggs, Kathryn Crouch, Leandro Lemgruber, Craig Lapsley, Richard McCulloch

PLOS Genetics: published December 13, 2018 | https://doi.org/10.1371/journal.pgen.1007729

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Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes

Heïdi Serra, Kyuha Choi, Xiaohui Zhao, Alexander R. Blackwell, Juhyun Kim, Ian R. Henderson

PLOS Genetics: published December 13, 2018 | https://doi.org/10.1371/journal.pgen.1007843

Biallelic mutations in nucleoporin NUP88 cause lethal fetal akinesia deformation sequence

Edith Bonnin, Pauline Cabochette, Alessandro Filosa, Ramona Jühlen, Shoko Komatsuzaki, Mohammed Hezwani, Achim Dickmanns, Valérie Martinelli, Marjorie Vermeersch, Lynn Supply, Nuno Martins, Laurence Pirenne, Gianina Ravenscroft, Marcus Lombard, Sarah Port, Christiane Spillner, Sandra Janssens, Ellen Roets, Jo Van Dorpe, Martin Lammens, Ralph H. Kehlenbach, Ralf Ficner, Nigel G. Laing, Katrin Hoffmann, Benoit Vanhollebeke, Birthe Fahrenkrog

PLOS Genetics: published December 13, 2018 | https://doi.org/10.1371/journal.pgen.1007845

miR-3607-3p suppresses non-small cell lung cancer (NSCLC) by targeting TGFBR1 and CCNE2

Peng Gao, Huan Wang, Jiarui Yu, Jie Zhang, Zhao Yang, Meiyue Liu, Yi Niu, Xiaomei Wei, Wei Wang, Hongmin Li, Yadi Wang, Guogui Sun

PLOS Genetics: published December 17, 2018 | https://doi.org/10.1371/journal.pgen.1007790

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The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea

David Schmidt, Hanna Reuter, Katja Hüttner, Larissa Ruhe, Franziska Rabert, Florian Seebeck, Manuel Irimia, Jordi Solana, Kerstin Bartscherer

PLOS Genetics: published December 17, 2018 | https://doi.org/10.1371/journal.pgen.1007828

regQTLs: Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors

Gary Wilk, Rosemary Braun

PLOS Genetics: published December 17, 2018 | https://doi.org/10.1371/journal.pgen.1007837

Evolution of maternal and zygotic mRNA complements in the early Drosophila embryo

Joel Atallah, Susan E. Lott

PLOS Genetics: published December 17, 2018 | https://doi.org/10.1371/journal.pgen.1007838

β-actin regulates a heterochromatin landscape essential for optimal induction of neuronal programs during direct reprograming

Xin Xie, Robertas Jankauskas, Aslam M. A. Mazari, Nizar Drou, Piergiorgio Percipalle

PLOS Genetics: published December 17, 2018 | https://doi.org/10.1371/journal.pgen.1007846

AMPK signaling linked to the schizophrenia-associated 1q21.1 deletion is required for neuronal and sleep maintenance

Stanislav Nagy, Gianna W. Maurer, Julie L. Hentze, Morten Rose, Thomas M. Werge, Kim Rewitz

PLOS Genetics: published December 19, 2018 | https://doi.org/10.1371/journal.pgen.1007623

Large-scale genome-wide meta-analysis of polycystic ovary syndrome suggests shared genetic architecture for different diagnosis criteria

Felix Day, Tugce Karaderi, Michelle R. Jones, Cindy Meun, Chunyan He, Alex Drong, Peter Kraft, Nan Lin, Hongyan Huang, Linda Broer, Reedik Magi, Richa Saxena, Triin Laisk, Margrit Urbanek, M. Geoffrey Hayes, Gudmar Thorleifsson, Juan Fernandez-Tajes, Anubha Mahajan, Benjamin H. Mullin, Bronwyn G. A. Stuckey, Timothy D. Spector, Scott G. Wilson, Mark O. Goodarzi, Lea Davis, Barbara Obermayer-Pietsch, André G. Uitterlinden, Verneri Anttila, Benjamin M. Neale, Marjo-Riitta Jarvelin, Bart Fauser, Irina Kowalska, Jenny A. Visser, Marianne Andersen, Ken Ong, Elisabet Stener-Victorin, David Ehrmann, Richard S. Legro, Andres Salumets, Mark I. McCarthy, Laure Morin-Papunen, Unnur Thorsteinsdottir, Kari Stefansson, the 23andMe Research Team, Unnur Styrkarsdottir, John R. B. Perry, Andrea Dunaif, Joop Laven, Steve Franks, Cecilia M. Lindgren, Corrine K. Welt

PLOS Genetics: published December 19, 2018 | https://doi.org/10.1371/journal.pgen.1007813

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RSM1, an Arabidopsis MYB protein, interacts with HY5/HYH to modulate seed germination and seedling development in response to abscisic acid and salinity

Bencan Yang, Zihao Song, Chaonan Li, Jiahao Jiang, Yangyang Zhou, Ruipu Wang, Qi Wang, Chang Ni, Qing Liang, Haodong Chen, Liu-Min Fan

PLOS Genetics: published December 19, 2018 | https://doi.org/10.1371/journal.pgen.1007839

Expression reflects population structure

Brielin C. Brown, Nicolas L. Bray, Lior Pachter

PLOS Genetics: published December 19, 2018 | https://doi.org/10.1371/journal.pgen.1007841

Distinguishing genetically between the germlines of male monozygotic twins

Michael Krawczak, Bruce Budowle, Jacqueline Weber-Lehmann, Burkhard Rolf

PLOS Genetics: published December 20, 2018 | https://doi.org/10.1371/journal.pgen.1007756

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Genetic exchanges are more frequent in bacteria encoding capsules

Olaya Rendueles, Jorge A. Moura de Sousa, Aude Bernheim, Marie Touchon, Eduardo P. C. Rocha

PLOS Genetics: published December 21, 2018 | https://doi.org/10.1371/journal.pgen.1007862

Comprehensive cross-disorder analyses of CNTNAP2 suggest it is unlikely to be a primary risk gene for psychiatric disorders

Claudio Toma, Kerrie D. Pierce, Alex D. Shaw, Anna Heath, Philip B. Mitchell, Peter R. Schofield, Janice M. Fullerton

PLOS Genetics: published December 26, 2018 | https://doi.org/10.1371/journal.pgen.1007535

Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers

Kerryn Elliott, Martin Boström, Stefan Filges, Markus Lindberg, Jimmy Van den Eynden, Anders Ståhlberg, Anders R. Clausen, Erik Larsson

PLOS Genetics: published December 26, 2018 | https://doi.org/10.1371/journal.pgen.1007849

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

Guy Nir, Irene Farabella, Cynthia Pérez Estrada, Carl G. Ebeling, Brian J. Beliveau, Hiroshi M. Sasaki, S. Dean Lee, Son C. Nguyen, Ruth B. McCole, Shyamtanu Chattoraj, Jelena Erceg, Jumana AlHaj Abed, Nuno M. C. Martins, Huy Q. Nguyen, Mohammed A. Hannan, Sheikh Russell, Neva C. Durand, Suhas S. P. Rao, Jocelyn Y. Kishi, Paula Soler-Vila, Michele Di Pierro, José N. Onuchic, Steven P. Callahan, John M. Schreiner, Jeff A. Stuckey, Peng Yin, Erez Lieberman Aiden, Marc A. Marti-Renom, C.-ting Wu

PLOS Genetics: published December 26, 2018 | https://doi.org/10.1371/journal.pgen.1007872

Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization model

Yuan Lu, Mikki Boswell, William Boswell, Susanne Kneitz, Barbara Klotz, Markita Savage, Raquel Salinas, Rebecca Marks, Janine Regneri, John Postlethwait, Wesley C. Warren, Manfred Schartl, Ronald Walter

PLOS Genetics: published December 26, 2018 | https://doi.org/10.1371/journal.pgen.1007875

Regulation of pollen lipid body biogenesis by MAP kinases and downstream WRKY transcription factors in Arabidopsis

Yueping Zheng, Xiangxiong Deng, Aili Qu, Mengmeng Zhang, Yuan Tao, Liuyi Yang, Yidong Liu, Juan Xu, Shuqun Zhang

PLOS Genetics: published December 26, 2018 | https://doi.org/10.1371/journal.pgen.1007880

On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses

Rebecca B. Harris, Andrew Sackman, Jeffrey D. Jensen

PLOS Genetics: published December 28, 2018 | https://doi.org/10.1371/journal.pgen.1007859

Genetic regulation of the placental transcriptome underlies birth weight and risk of childhood obesity

Shouneng Peng, Maya A. Deyssenroth, Antonio F. Di Narzo, Haoxiang Cheng, Zhongyang Zhang, Luca Lambertini, Arno Ruusalepp, Jason C. Kovacic, Johan L. M. Bjorkegren, Carmen J. Marsit, Jia Chen, Ke Hao

PLOS Genetics: published December 31, 2018 | https://doi.org/10.1371/journal.pgen.1007799

Bayesian multiple logistic regression for case-control GWAS

Saikat Banerjee, Lingyao Zeng, Heribert Schunkert, Johannes Söding

PLOS Genetics: published December 31, 2018 | https://doi.org/10.1371/journal.pgen.1007856

Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi

Valentina del Olmo Toledo, Robert Puccinelli, Polly M. Fordyce, J. Christian Pérez

PLOS Genetics: published December 31, 2018 | https://doi.org/10.1371/journal.pgen.1007884

Corrections

Correction: Association analysis using somatic mutations

Yang Liu, Qianchuan He, Wei Sun

PLOS Genetics: published December 6, 2018 | https://doi.org/10.1371/journal.pgen.1007848

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Correction: Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV

Kristof Theys, Alison F. Feder, Maoz Gelbart, Marion Hartl, Adi Stern, Pleuni S. Pennings

PLOS Genetics: published December 10, 2018 | https://doi.org/10.1371/journal.pgen.1007855

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Correction: Loss of the BMP Antagonist, SMOC-1, Causes Ophthalmo-Acromelic (Waardenburg Anophthalmia) Syndrome in Humans and Mice

Joe Rainger, Ellen van Beusekom, Jacqueline K. Ramsay, Lisa McKie, Lihadh Al-Gazali, Rosanna Pallotta, Anita Saponari, Peter Branney, Malcolm Fisher, Harris Morrison, Louise Bicknell, Philippe Gautier, Paul Perry, Kishan Sokhi, David Sexton, Tanya M. Bardakjian, Adele S. Schneider, Nursel Elcioglu, Ferda Ozkinay, Rainer Koenig, Andre Mégarbané, C. Nur Semerci, Ayesha Khan, Saemah Zafar, Raoul Hennekam, Sérgio B. Sousa, Lina Ramos, Livia Garavelli, Andrea Superti Furga, Anita Wischmeijer, Ian J. Jackson, Gabriele Gillessen-Kaesbach, Han G. Brunner, Dagmar Wieczorek, Hans van Bokhoven, David R. FitzPatrick

PLOS Genetics: published December 26, 2018 | https://doi.org/10.1371/journal.pgen.1007866

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Topic Page

Micropeptide

Maria E. Sousa, Michael H. Farkas

PLOS Genetics: published December 13, 2018 | https://doi.org/10.1371/journal.pgen.1007764