February 2012

Holoprosencephaly is a severe genetic disease affecting human brain and craniofacial development. The work by Taniguchi et al. demonstrates that Tgif1, a gene implicated in human holoprosencephaly, is involved in regulating Sonic Hedgehog signaling and forebrain development during early mouse embryogenesis. This image shows a scanning electron micrograph of the frontal view of a normal mouse embryo at nine days post fertilization.

Image Credit: Kenichiro Taniguchi and David Wotton (University of Virginia).

Perspectives

Upsetting the Dogma: Germline Selection in Human Males

James F. Crow

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002535

The Williams-Beuren Syndrome—A Window into Genetic Variants Leading to the Development of Cardiovascular Disease

Gregory N. Adams, Alvin H. Schmaier

PLOS Genetics: published February 2, 2012 | https://doi.org/10.1371/journal.pgen.1002479

Diced Triplets Expose Neurons to RISC

Dobrila D. Rudnicki, Russell L. Margolis, Christopher E. Pearson, Wlodzimierz J. Krzyzosiak

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002545

Research Articles

Positive Selection for New Disease Mutations in the Human Germline: Evidence from the Heritable Cancer Syndrome Multiple Endocrine Neoplasia Type 2B

Soo-Kyung Choi, Song-Ro Yoon, Peter Calabrese, Norman Arnheim

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002420

Genomic Restructuring in the Tasmanian Devil Facial Tumour: Chromosome Painting and Gene Mapping Provide Clues to Evolution of a Transmissible Tumour

Janine E. Deakin, Hannah S. Bender, Anne-Maree Pearse, Willem Rens, Patricia C. M. O'Brien, Malcolm A. Ferguson-Smith, Yuanyuan Cheng, Katrina Morris, Robyn Taylor, Andrew Stuart, Katherine Belov, Chris T. Amemiya, Elizabeth P. Murchison, Anthony T. Papenfuss, Jennifer A. Marshall Graves

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002483

Genome-Wide Association Study Identifies Novel Loci Associated with Circulating Phospho- and Sphingolipid Concentrations

Ayşe Demirkan, Cornelia M. van Duijn, Peter Ugocsai, Aaron Isaacs, Peter P. Pramstaller, Gerhard Liebisch, James F. Wilson, Åsa Johansson, Igor Rudan, Yurii S. Aulchenko, Anatoly V. Kirichenko, A. Cecile J. W. Janssens, Ritsert C. Jansen, Carsten Gnewuch, Francisco S. Domingues, Cristian Pattaro, Sarah H. Wild, Inger Jonasson, Ozren Polasek, Irina V. Zorkoltseva, Albert Hofman, Lennart C. Karssen, Maksim Struchalin, James Floyd, Wilmar Igl, Zrinka Biloglav, Linda Broer, Arne Pfeufer, Irene Pichler, Susan Campbell, Ghazal Zaboli, Ivana Kolcic, Fernando Rivadeneira, Jennifer Huffman, Nicholas D. Hastie, Andre Uitterlinden, Lude Franke, Christopher S. Franklin, Veronique Vitart, DIAGRAM Consortium, Christopher P. Nelson, Michael Preuss, CARDIoGRAM Consortium, Joshua C. Bis, Christopher J. O'Donnell, Nora Franceschini, CHARGE Consortium, Jacqueline C. M. Witteman, Tatiana Axenovich, Ben A. Oostra, Thomas Meitinger, Andrew A. Hicks, Caroline Hayward, Alan F. Wright, Ulf Gyllensten, Harry Campbell, Gerd Schmitz, on behalf of the EUROSPAN consortium

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002490

Computational Prediction and Molecular Characterization of an Oomycete Effector and the Cognate Arabidopsis Resistance Gene

Sandra Goritschnig, Ksenia V. Krasileva, Douglas Dahlbeck, Brian J. Staskawicz

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002502

A Strong Deletion Bias in Nonallelic Gene Conversion

Raquel Assis, Alexey S. Kondrashov

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002508

Nondisjunction of a Single Chromosome Leads to Breakage and Activation of DNA Damage Checkpoint in G2

Oliver Quevedo, Jonay García-Luis, Emiliano Matos-Perdomo, Luis Aragón, Félix Machín

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002509

Psoriasis Patients Are Enriched for Genetic Variants That Protect against HIV-1 Disease

Haoyan Chen, Genki Hayashi, Olivia Y. Lai, Alexander Dilthey, Peter J. Kuebler, Tami V. Wong, Maureen P. Martin, Marcelo A. Fernandez Vina, Gil McVean, Matthias Wabl, Kieron S. Leslie, Toby Maurer, Jeffrey N. Martin, Steven G. Deeks, Mary Carrington, Anne M. Bowcock, Douglas F. Nixon, Wilson Liao

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002514

Repression of a Potassium Channel by Nuclear Hormone Receptor and TGF-β Signaling Modulates Insulin Signaling in Caenorhabditis elegans

Donha Park, Karen L. Jones, Hyojin Lee, Terrance P. Snutch, Stefan Taubert, Donald L. Riddle

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002519

Discovery of a Modified Tetrapolar Sexual Cycle in Cryptococcus amylolentus and the Evolution of MAT in the Cryptococcus Species Complex

Keisha Findley, Sheng Sun, James A. Fraser, Yen-Ping Hsueh, Anna Floyd Averette, Wenjun Li, Fred S. Dietrich, Joseph Heitman

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002528

The Origin and Nature of Tightly Clustered BTG1 Deletions in Precursor B-Cell Acute Lymphoblastic Leukemia Support a Model of Multiclonal Evolution

Esmé Waanders, Blanca Scheijen, Laurens T. van der Meer, Simon V. van Reijmersdal, Liesbeth van Emst, Yvet Kroeze, Edwin Sonneveld, Peter M. Hoogerbrugge, Ad Geurts van Kessel, Frank N. van Leeuwen, Roland P. Kuiper

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002533

The Retrohoming of Linear Group II Intron RNAs in Drosophila melanogaster Occurs by Both DNA Ligase 4–Dependent and –Independent Mechanisms

Travis B. White, Alan M. Lambowitz

PLOS Genetics: published February 16, 2012 | https://doi.org/10.1371/journal.pgen.1002534

Systematic Detection of Epistatic Interactions Based on Allele Pair Frequencies

Marit Ackermann, Andreas Beyer

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002463

Familial Identification: Population Structure and Relationship Distinguishability

Rori V. Rohlfs, Stephanie Malia Fullerton, Bruce S. Weir

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002469

Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA

Andrea D. McCue, Saivageethi Nuthikattu, Sarah H. Reeder, R. Keith Slotkin

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002474

Structural Basis of Transcriptional Gene Silencing Mediated by Arabidopsis MOM1

Taisuke Nishimura, Guillaume Molinard, Tom J. Petty, Larissa Broger, Caroline Gabus, Thanos D. Halazonetis, Stéphane Thore, Jerzy Paszkowski

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002484

Phosphorylation of Chromosome Core Components May Serve as Axis Marks for the Status of Chromosomal Events during Mammalian Meiosis

Tomoyuki Fukuda, Florencia Pratto, John C. Schimenti, James M. A. Turner, R. Daniel Camerini-Otero, Christer Höög

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002485

Contrasting Properties of Gene-Specific Regulatory, Coding, and Copy Number Mutations in Saccharomyces cerevisiae: Frequency, Effects, and Dominance

Jonathan D. Gruber, Kara Vogel, Gizem Kalay, Patricia J. Wittkopp

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002497

A Regulatory Network for Coordinated Flower Maturation

Paul H. Reeves, Christine M. Ellis, Sara E. Ploense, Miin-Feng Wu, Vandana Yadav, Dorothea Tholl, Aurore Chételat, Ina Haupt, Brian J. Kennerley, Charles Hodgens, Edward E. Farmer, Punita Nagpal, Jason W. Reed

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002506

Rewiring of PDZ Domain-Ligand Interaction Network Contributed to Eukaryotic Evolution

Jinho Kim, Inhae Kim, Jae-Seong Yang, Young-Eun Shin, Jihye Hwang, Solip Park, Yoon Sup Choi, Sanguk Kim

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002510

Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum

Nigel F. Delaney, Susan Balenger, Camille Bonneaud, Christopher J. Marx, Geoffrey E. Hill, Naola Ferguson-Noel, Peter Tsai, Allen Rodrigo, Scott V. Edwards

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002511

Neurophysiological Defects and Neuronal Gene Deregulation in Drosophila mir-124 Mutants

Kailiang Sun, Jakub Orzechowski Westholm, Kazuya Tsurudome, Joshua W. Hagen, Yubing Lu, Minoree Kohwi, Doron Betel, Fen-Biao Gao, A. Pejmun Haghighi, Chris Q. Doe, Eric C. Lai

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002515

The Dynamics and Prognostic Potential of DNA Methylation Changes at Stem Cell Gene Loci in Women's Cancer

Joanna Zhuang, Allison Jones, Shih-Han Lee, Esther Ng, Heidi Fiegl, Michal Zikan, David Cibula, Alexandra Sargent, Helga B. Salvesen, Ian J. Jacobs, Henry C. Kitchener, Andrew E. Teschendorff, Martin Widschwendter

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002517

Negative Supercoiling Creates Single-Stranded Patches of DNA That Are Substrates for AID–Mediated Mutagenesis

Jahan-Yar Parsa, Shaliny Ramachandran, Ahmad Zaheen, Rajeev M. Nepal, Anat Kapelnikov, Antoaneta Belcheva, Maribel Berru, Diana Ronai, Alberto Martin

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002518

Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders

Claire S. Leblond, Jutta Heinrich, Richard Delorme, Christian Proepper, Catalina Betancur, Guillaume Huguet, Marina Konyukh, Pauline Chaste, Elodie Ey, Maria Rastam, Henrik Anckarsäter, Gudrun Nygren, I. Carina Gillberg, Jonas Melke, Roberto Toro, Beatrice Regnault, Fabien Fauchereau, Oriane Mercati, Nathalie Lemière, David Skuse, Martin Poot, Richard Holt, Anthony P. Monaco, Irma Järvelä, Katri Kantojärvi, Raija Vanhala, Sarah Curran, David A. Collier, Patrick Bolton, Andreas Chiocchetti, Sabine M. Klauck, Fritz Poustka, Christine M. Freitag, Regina Waltes, Marnie Kopp, Eftichia Duketis, Elena Bacchelli, Fiorella Minopoli, Liliana Ruta, Agatino Battaglia, Luigi Mazzone, Elena Maestrini, Ana F. Sequeira, Barbara Oliveira, Astrid Vicente, Guiomar Oliveira, Dalila Pinto, Stephen W. Scherer, Diana Zelenika, Marc Delepine, Mark Lathrop, Dominique Bonneau, Vincent Guinchat, Françoise Devillard, Brigitte Assouline, Marie-Christine Mouren, Marion Leboyer, Christopher Gillberg, Tobias M. Boeckers, Thomas Bourgeron

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002521

Mixed Effects Modeling of Proliferation Rates in Cell-Based Models: Consequence for Pharmacogenomics and Cancer

Hae Kyung Im, Eric R. Gamazon, Amy L. Stark, R. Stephanie Huang, Nancy J. Cox, M. Eileen Dolan

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002525

GTPase Activity and Neuronal Toxicity of Parkinson's Disease–Associated LRRK2 Is Regulated by ArfGAP1

Klodjan Stafa, Alzbeta Trancikova, Philip J. Webber, Liliane Glauser, Andrew B. West, Darren J. Moore

PLOS Genetics: published February 9, 2012 | https://doi.org/10.1371/journal.pgen.1002526

Reduction of NADPH-Oxidase Activity Ameliorates the Cardiovascular Phenotype in a Mouse Model of Williams-Beuren Syndrome

Victoria Campuzano, Maria Segura-Puimedon, Verena Terrado, Carolina Sánchez-Rodríguez, Mathilde Coustets, Mauricio Menacho-Márquez, Julián Nevado, Xosé R. Bustelo, Uta Francke, Luis A. Pérez-Jurado

PLOS Genetics: published February 2, 2012 | https://doi.org/10.1371/journal.pgen.1002458

Evaluation of the Role of Functional Constraints on the Integrity of an Ultraconserved Region in the Genus Drosophila

Carlos Díaz-Castillo, Xiao-Qin Xia, José M. Ranz

PLOS Genetics: published February 2, 2012 | https://doi.org/10.1371/journal.pgen.1002475

The Mitochondrial Chaperone Protein TRAP1 Mitigates α-Synuclein Toxicity

Erin K. Butler, Aaron Voigt, A. Kathrin Lutz, Jane P. Toegel, Ellen Gerhardt, Peter Karsten, Björn Falkenburger, Andrea Reinartz, Konstanze F. Winklhofer, Jörg B. Schulz

PLOS Genetics: published February 2, 2012 | https://doi.org/10.1371/journal.pgen.1002488

Loss of Function of the Cik1/Kar3 Motor Complex Results in Chromosomes with Syntelic Attachment That Are Sensed by the Tension Checkpoint

Fengzhi Jin, Hong Liu, Ping Li, Hong-Guo Yu, Yanchang Wang

PLOS Genetics: published February 2, 2012 | https://doi.org/10.1371/journal.pgen.1002492

Down-Regulating Sphingolipid Synthesis Increases Yeast Lifespan

Xinhe Huang, Jun Liu, Robert C. Dickson

PLOS Genetics: published February 2, 2012 | https://doi.org/10.1371/journal.pgen.1002493

The Empirical Power of Rare Variant Association Methods: Results from Sanger Sequencing in 1,998 Individuals

Martin Ladouceur, Zari Dastani, Yurii S. Aulchenko, Celia M. T. Greenwood, J. Brent Richards

PLOS Genetics: published February 2, 2012 | https://doi.org/10.1371/journal.pgen.1002496

Raf1 Is a DCAF for the Rik1 DDB1-Like Protein and Has Separable Roles in siRNA Generation and Chromatin Modification

Alessia Buscaino, Sharon A. White, Douglas R. Houston, Erwan Lejeune, Femke Simmer, Flavia de Lima Alves, Piyush T. Diyora, Takeshi Urano, Elizabeth H. Bayne, Juri Rappsilber, Robin C. Allshire

PLOS Genetics: published February 2, 2012 | https://doi.org/10.1371/journal.pgen.1002499

Inter-Homolog Crossing-Over and Synapsis in Arabidopsis Meiosis Are Dependent on the Chromosome Axis Protein AtASY3

Maheen Ferdous, James D. Higgins, Kim Osman, Christophe Lambing, Elisabeth Roitinger, Karl Mechtler, Susan J. Armstrong, Ruth Perry, Mónica Pradillo, Nieves Cuñado, F. Chris H. Franklin

PLOS Genetics: published February 2, 2012 | https://doi.org/10.1371/journal.pgen.1002507

Cell Lineage Analysis of the Mammalian Female Germline

Yitzhak Reizel, Shalev Itzkovitz, Rivka Adar, Judith Elbaz, Adrian Jinich, Noa Chapal-Ilani, Yosef E. Maruvka, Nava Nevo, Zipora Marx, Inna Horovitz, Adam Wasserstrom, Avi Mayo, Irena Shur, Dafna Benayahu, Karl Skorecki, Eran Segal, Nava Dekel, Ehud Shapiro

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002477

A Pathogenic Mechanism in Huntington's Disease Involves Small CAG-Repeated RNAs with Neurotoxic Activity

Mónica Bañez-Coronel, Silvia Porta, Birgit Kagerbauer, Elisabet Mateu-Huertas, Lorena Pantano, Isidre Ferrer, Manuel Guzmán, Xavier Estivill, Eulàlia Martí

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002481

Msx Homeobox Genes Critically Regulate Embryo Implantation by Controlling Paracrine Signaling between Uterine Stroma and Epithelium

Shanmugasundaram Nallasamy, Quanxi Li, Milan K. Bagchi, Indrani C. Bagchi

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002500

Developmental Transcriptional Networks Are Required to Maintain Neuronal Subtype Identity in the Mature Nervous System

Kevin T. Eade, Hailey A. Fancher, Marc S. Ridyard, Douglas W. Allan

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002501

The Role of Glypicans in Wnt Inhibitory Factor-1 Activity and the Structural Basis of Wif1's Effects on Wnt and Hedgehog Signaling

Andrei Avanesov, Shawn M. Honeyager, Jarema Malicki, Seth S. Blair

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002503

Coexpression Network Analysis in Abdominal and Gluteal Adipose Tissue Reveals Regulatory Genetic Loci for Metabolic Syndrome and Related Phenotypes

Josine L. Min, George Nicholson, Ingileif Halgrimsdottir, Kristian Almstrup, Andreas Petri, Amy Barrett, Mary Travers, Nigel W. Rayner, Reedik Mägi, Fredrik H. Pettersson, John Broxholme, Matt J. Neville, Quin F. Wills, Jane Cheeseman, The GIANT Consortium, The MolPAGE Consortium, Maxine Allen, Chris C. Holmes, Tim D. Spector, Jan Fleckner, Mark I. McCarthy, Fredrik Karpe, Cecilia M. Lindgren, Krina T. Zondervan

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002505

The Caenorhabditis elegans Eph Receptor Activates NCK and N-WASP, and Inhibits Ena/VASP to Regulate Growth Cone Dynamics during Axon Guidance

Ahmed M. Mohamed, Jeffrey R. Boudreau, Fabian P. S. Yu, Jun Liu, Ian D. Chin-Sang

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002513

Genome-Wide Association Study Identifies Chromosome 10q24.32 Variants Associated with Arsenic Metabolism and Toxicity Phenotypes in Bangladesh

Brandon L. Pierce, Muhammad G. Kibriya, Lin Tong, Farzana Jasmine, Maria Argos, Shantanu Roy, Rachelle Paul-Brutus, Ronald Rahaman, Muhammad Rakibuz-Zaman, Faruque Parvez, Alauddin Ahmed, Iftekhar Quasem, Samar K. Hore, Shafiul Alam, Tariqul Islam, Vesna Slavkovich, Mary V. Gamble, Md Yunus, Mahfuzar Rahman, John A. Baron, Joseph H. Graziano, Habibul Ahsan

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002522

Association of a Functional Variant in the Wnt Co-Receptor LRP6 with Early Onset Ileal Crohn's Disease

Maureen J. Koslowski, Zora Teltschik, Julia Beisner, Elke Schaeffeler, Guoxing Wang, Irmgard Kübler, Michael Gersemann, Rachel Cooney, Derek Jewell, Walter Reinisch, Séverine Vermeire, Paul Rutgeerts, Matthias Schwab, Eduard F. Stange, Jan Wehkamp

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002523

Loss of Tgif Function Causes Holoprosencephaly by Disrupting the Shh Signaling Pathway

Kenichiro Taniguchi, Anoush E. Anderson, Ann E. Sutherland, David Wotton

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002524

Sequestration of Highly Expressed mRNAs in Cytoplasmic Granules, P-Bodies, and Stress Granules Enhances Cell Viability

Anna Lavut, Dina Raveh

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002527

Genome-Wide Association Study in East Asians Identifies Novel Susceptibility Loci for Breast Cancer

Jirong Long, Qiuyin Cai, Hyuna Sung, Jiajun Shi, Ben Zhang, Ji-Yeob Choi, Wanqing Wen, Ryan J. Delahanty, Wei Lu, Yu-Tang Gao, Hongbing Shen, Sue K. Park, Kexin Chen, Chen-Yang Shen, Zefang Ren, Christopher A. Haiman, Keitaro Matsuo, Mi Kyung Kim, Ui Soon Khoo, Motoki Iwasaki, Ying Zheng, Yong-Bing Xiang, Kai Gu, Nathaniel Rothman, Wenjing Wang, Zhibin Hu, Yao Liu, Keun-Young Yoo, Dong-Young Noh, Bok-Ghee Han, Min Hyuk Lee, Hong Zheng, Lina Zhang, Pei-Ei Wu, Ya-Lan Shieh, Sum Yin Chan, Shenming Wang, Xiaoming Xie, Sung-Won Kim, Brian E. Henderson, Loic Le Marchand, Hidemi Ito, Yoshio Kasuga, Sei-Hyun Ahn, Han Sung Kang, Kelvin Y. K. Chan, Hiroji Iwata, Shoichiro Tsugane, Chun Li, Xiao-Ou Shu, Dae-Hee Kang, Wei Zheng

PLOS Genetics: published February 23, 2012 | https://doi.org/10.1371/journal.pgen.1002532

Cover

Anterior development during early mouse embryogenesis.

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