February 2013

The mismatch repair protein MSH3 is required to drive disease-causing CAG/CTG repeat expansions in Huntington's disease and myotonic dystrophy mice, contrary to its canonical role of mutation avoidance, making MSH3 the major modifier of repeat instability. In this issue, Tomé and colleagues identify mouse strain-specific variants of Msh3 that modify MSH3 protein levels, which dramatically modify levels of tissue-specific CAG repeat instability, much like a tuning dial modifies the volume of music from a stereo amplifier (as imaged). Since levels of somatic CAG expansions can modulate disease onset, progression, and severity, specific DNA repair gene variants may have prognostic implications.

Image Credit: Christopher E. Pearson and Colin T. Pearson, The Hospital for Sick Children.

Viewpoints

Comment on “Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome”

Corey T. Watson, Paras Garg, Andrew J. Sharp

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003332

Confounding by Repetitive Elements and CpG Islands Does Not Explain the Association between Hypomethylation and Genomic Instability

R. Alan Harris, Chad Shaw, Jian Li, Sau Wai Cheung, Cristian Coarfa, Mira Jeong, Margaret A. Goodell, Lisa D. White, Ankita Patel, Sung-Hae Kang, A. Craig Chinault, Tomasz Gambin, Anna Gambin, James R. Lupski, Aleksandar Milosavljevic

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003333

Perspective

Retrotransposon Activates Ectopic Ptf1 Expression: A Short Tail

Bruce A. Hamilton

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003331

Research Articles

Rearrangements of 2.5 Kilobases of Noncoding DNA from the Drosophila even-skipped Locus Define Predictive Rules of Genomic cis-Regulatory Logic

Ah-Ram Kim, Carlos Martinez, John Ionides, Alexandre F. Ramos, Michael Z. Ludwig, Nobuo Ogawa, David H. Sharp, John Reinitz

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003243

The Interaction of CtIP and Nbs1 Connects CDK and ATM to Regulate HR–Mediated Double-Strand Break Repair

Hailong Wang, Linda Z. Shi, Catherine C. L. Wong, Xuemei Han, Patty Yi-Hwa Hwang, Lan N. Truong, Qingyuan Zhu, Zhengping Shao, David J. Chen, Michael W. Berns, John R. Yates III, Longchuan Chen, Xiaohua Wu

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003277

MSH3 Polymorphisms and Protein Levels Affect CAG Repeat Instability in Huntington's Disease Mice

Stéphanie Tomé, Kevin Manley, Jodie P. Simard, Greg W. Clark, Meghan M. Slean, Meera Swami, Peggy F. Shelbourne, Elisabeth R. M. Tillier, Darren G. Monckton, Anne Messer, Christopher E. Pearson

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003280

Cell Reprogramming Requires Silencing of a Core Subset of Polycomb Targets

Giulia Fragola, Pierre-Luc Germain, Pasquale Laise, Alessandro Cuomo, Alessandro Blasimme, Fridolin Gross, Elena Signaroldi, Gabriele Bucci, Cesar Sommer, Giancarlo Pruneri, Giovanni Mazzarol, Tiziana Bonaldi, Gustavo Mostoslavsky, Stefano Casola, Giuseppe Testa

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003292

An Evolutionary Perspective on Epistasis and the Missing Heritability

Gibran Hemani, Sara Knott, Chris Haley

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003295

Genome-Wide Analysis Points to Roles for Extracellular Matrix Remodeling, the Visual Cycle, and Neuronal Development in Myopia

Amy K. Kiefer, Joyce Y. Tung, Chuong B. Do, David A. Hinds, Joanna L. Mountain, Uta Francke, Nicholas Eriksson

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003299

Deleterious Alleles in the Human Genome Are on Average Younger Than Neutral Alleles of the Same Frequency

Adam Kiezun, Sara L. Pulit, Laurent C. Francioli, Freerk van Dijk, Morris Swertz, Dorret I. Boomsma, Cornelia M. van Duijn, P. Eline Slagboom, G. J. B. van Ommen, Cisca Wijmenga, Genome of the Netherlands Consortium, Paul I. W. de Bakker, Shamil R. Sunyaev

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003301

FAM20A Mutations Can Cause Enamel-Renal Syndrome (ERS)

Shih-Kai Wang, Parissa Aref, Yuanyuan Hu, Rachel N. Milkovich, James P. Simmer, Mohammad El-Khateeb, Hinda Daggag, Zaid H. Baqain, Jan C-C. Hu

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003302

JNK-Interacting Protein 3 Mediates the Retrograde Transport of Activated c-Jun N-Terminal Kinase and Lysosomes

Catherine M. Drerup, Alex V. Nechiporuk

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003303

Dynamic Association of NUP98 with the Human Genome

Yun Liang, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, Martin W. Hetzer

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003308

A Genome-Wide RNAi Screen in Caenorhabditis elegans Identifies the Nicotinic Acetylcholine Receptor Subunit ACR-7 as an Antipsychotic Drug Target

Taixiang Saur, Sarah E. DeMarco, Angelica Ortiz, Gregory R. Sliwoski, Limin Hao, Xin Wang, Bruce M. Cohen, Edgar A. Buttner

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003313

Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture

Marc Haber, Dominique Gauguier, Sonia Youhanna, Nick Patterson, Priya Moorjani, Laura R. Botigué, Daniel E. Platt, Elizabeth Matisoo-Smith, David F. Soria-Hernanz, R. Spencer Wells, Jaume Bertranpetit, Chris Tyler-Smith, David Comas, Pierre A. Zalloua

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003316

ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies

Gabriel E. Zentner, Toshio Tsukiyama, Steven Henikoff

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003317

Coordination of Chromatid Separation and Spindle Elongation by Antagonistic Activities of Mitotic and S-Phase CDKs

Fengshan Liang, Daniel Richmond, Yanchang Wang

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003319

Conditional Inactivation of the DNA Damage Response Gene Hus1 in Mouse Testis Reveals Separable Roles for Components of the RAD9-RAD1-HUS1 Complex in Meiotic Chromosome Maintenance

Amy M. Lyndaker, Pei Xin Lim, Joanna M. Mleczko, Catherine E. Diggins, J. Kim Holloway, Rebecca J. Holmes, Rui Kan, Donald H. Schlafer, Raimundo Freire, Paula E. Cohen, Robert S. Weiss

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003320

Gene-Based Testing of Interactions in Association Studies of Quantitative Traits

Li Ma, Andrew G. Clark, Alon Keinan

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003321

Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci

Christopher L. Schardl, Carolyn A. Young, Uljana Hesse, Stefan G. Amyotte, Kalina Andreeva, Patrick J. Calie, Damien J. Fleetwood, David C. Haws, Neil Moore, Birgitt Oeser, Daniel G. Panaccione, Kathryn K. Schweri, Christine R. Voisey, Mark L. Farman, Jerzy W. Jaromczyk, Bruce A. Roe, Donal M. O'Sullivan, Barry Scott, Paul Tudzynski, Zhiqiang An, Elissaveta G. Arnaoudova, Charles T. Bullock, Nikki D. Charlton, Li Chen, Murray Cox, Randy D. Dinkins, Simona Florea, Anthony E. Glenn, Anna Gordon, Ulrich Güldener, Daniel R. Harris, Walter Hollin, Jolanta Jaromczyk, Richard D. Johnson, Anar K. Khan, Eckhard Leistner, Adrian Leuchtmann, Chunjie Li, JinGe Liu, Jinze Liu, Miao Liu, Wade Mace, Caroline Machado, Padmaja Nagabhyru, Juan Pan, Jan Schmid, Koya Sugawara, Ulrike Steiner, Johanna E. Takach, Eiji Tanaka, Jennifer S. Webb, Ella V. Wilson, Jennifer L. Wiseman, Ruriko Yoshida, Zheng Zeng

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003323

Roles of the Developmental Regulator unc-62/Homothorax in Limiting Longevity in Caenorhabditis elegans

Eric L. Van Nostrand, Adolfo Sánchez-Blanco, Beijing Wu, Andy Nguyen, Stuart K. Kim

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003325

Age-Dependent Transition from Cell-Level to Population-Level Control in Murine Intestinal Homeostasis Revealed by Coalescence Analysis

Zheng Hu, Yun-Xin Fu, Anthony J. Greenberg, Chung-I Wu, Weiwei Zhai

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003326

Quantitative Analysis of Histone Modifications: Formaldehyde Is a Source of Pathological N⁶-Formyllysine That Is Refractory to Histone Deacetylases

Bahar Edrissi, Koli Taghizadeh, Peter C. Dedon

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003328

The Amidation Step of Diphthamide Biosynthesis in Yeast Requires DPH6, a Gene Identified through Mining the DPH1-DPH5 Interaction Network

Shanow Uthman, Christian Bär, Viktor Scheidt, Shihui Liu, Sara ten Have, Flaviano Giorgini, Michael J. R. Stark, Raffael Schaffrath

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003334

MicroRNA-3148 Modulates Allelic Expression of Toll-Like Receptor 7 Variant Associated with Systemic Lupus Erythematosus

Yun Deng, Jian Zhao, Daisuke Sakurai, Kenneth M. Kaufman, Jeffrey C. Edberg, Robert P. Kimberly, Diane L. Kamen, Gary S. Gilkeson, Chaim O. Jacob, R. Hal Scofield, Carl D. Langefeld, Jennifer A. Kelly, Rosalind Ramsey-Goldman, Michelle A. Petri, John D. Reveille, Luis M. Vilá, Graciela S. Alarcón, Timothy J. Vyse, Bernardo A. Pons-Estel, on behalf of the Argentine Collaborative Group, Barry I. Freedman, Patrick M. Gaffney, Kathy Moser Sivils, Judith A. James, Peter K. Gregersen, Juan-Manuel Anaya, Timothy B. Niewold, Joan T. Merrill, Lindsey A. Criswell, Anne M. Stevens, Susan A. Boackle, Rita M. Cantor, Weiling Chen, Jeniffer M. Grossman, Bevra H. Hahn, John B. Harley, Marta E. Alarcόn-Riquelme, on behalf of the BIOLUPUS and GENLES networks, Elizabeth E. Brown, Betty P. Tsao

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003336

CELF Family RNA–Binding Protein UNC-75 Regulates Two Sets of Mutually Exclusive Exons of the unc-32 Gene in Neuron-Specific Manners in Caenorhabditis elegans

Hidehito Kuroyanagi, Yohei Watanabe, Masatoshi Hagiwara

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003337

Ectopic Expression of Ptf1a Induces Spinal Defects, Urogenital Defects, and Anorectal Malformations in Danforth's Short Tail Mice

Kei Semba, Kimi Araki, Ken-ichirou Matsumoto, Hiroko Suda, Takashi Ando, Akira Sei, Hiroshi Mizuta, Katsumasa Takagi, Mai Nakahara, Mayumi Muta, Gen Yamada, Naomi Nakagata, Aritoshi Iida, Shiro Ikegawa, Yusuke Nakamura, Masatake Araki, Kuniya Abe, Ken-ichi Yamamura

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003204

Next-Generation Sequencing Identifies the Danforth's Short Tail Mouse Mutation as a Retrotransposon Insertion Affecting Ptf1a Expression

Christopher N. Vlangos, Amanda N. Siuniak, Dan Robinson, Arul M. Chinnaiyan, Robert H. Lyons Jr, James D. Cavalcoli, Catherine E. Keegan

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003205

A Retrotransposon Insertion in the 5′ Regulatory Domain of Ptf1a Results in Ectopic Gene Expression and Multiple Congenital Defects in Danforth's Short Tail Mouse

Francesca Lugani, Ripla Arora, Natalia Papeta, Ami Patel, Zongyu Zheng, Roel Sterken, Ruth A. Singer, Gianluca Caridi, Cathy Mendelsohn, Lori Sussel, Virginia E. Papaioannou, Ali G. Gharavi

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003206

Lessons from Dwarf8 on the Strengths and Weaknesses of Structured Association Mapping

Sara J. Larsson, Alexander E. Lipka, Edward S. Buckler

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003246

Genetic Determinants of Trabecular and Cortical Volumetric Bone Mineral Densities and Bone Microstructure

Lavinia Paternoster, Mattias Lorentzon, Terho Lehtimäki, Joel Eriksson, Mika Kähönen, Olli Raitakari, Marika Laaksonen, Harri Sievänen, Jorma Viikari, Leo-Pekka Lyytikäinen, Dan Mellström, Magnus Karlsson, Östen Ljunggren, Elin Grundberg, John P. Kemp, Adrian Sayers, Maria Nethander, David M. Evans, Liesbeth Vandenput, Jon H. Tobias, Claes Ohlsson

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003247

Properties and Modeling of GWAS when Complex Disease Risk Is Due to Non-Complementing, Deleterious Mutations in Genes of Large Effect

Kevin R. Thornton, Andrew J. Foran, Anthony D. Long

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003258

Ehd4 Encodes a Novel and Oryza-Genus-Specific Regulator of Photoperiodic Flowering in Rice

He Gao, Xiao-Ming Zheng, Guilin Fei, Jun Chen, Mingna Jin, Yulong Ren, Weixun Wu, Kunneng Zhou, Peike Sheng, Feng Zhou, Ling Jiang, Jie Wang, Xin Zhang, Xiuping Guo, Jiu-Lin Wang, Zhijun Cheng, Chuanyin Wu, Haiyang Wang, Jian-Min Wan

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003281

PcG-Mediated Higher-Order Chromatin Structures Modulate Replication Programs at the Drosophila BX-C

Federica Lo Sardo, Chiara Lanzuolo, Federico Comoglio, Marco De Bardi, Renato Paro, Valerio Orlando

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003283

SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

Michael A. Lodato, Christopher W. Ng, Joseph A. Wamstad, Albert W. Cheng, Kevin K. Thai, Ernest Fraenkel, Rudolf Jaenisch, Laurie A. Boyer

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003288

Patterning of Leaf Vein Networks by Convergent Auxin Transport Pathways

Megan G. Sawchuk, Alexander Edgar, Enrico Scarpella

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003294

Discovery of a Splicing Regulator Required for Cell Cycle Progression

Elena S. Suvorova, Matthew Croken, Stella Kratzer, Li-Min Ting, Magnolia Conde de Felipe, Bharath Balu, Meng L. Markillie, Louis M. Weiss, Kami Kim, Michael W. White

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003305

Mechanisms Involved in the Functional Divergence of Duplicated GroEL Chaperonins in Myxococcus xanthus DK1622

Yan Wang, Wen-yan Zhang, Zheng Zhang, Jian Li, Zhi-feng Li, Zai-gao Tan, Tian-tian Zhang, Zhi-hong Wu, Hong Liu, Yue-zhong Li

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003306

The Caenorhabditis elegans JNK Signaling Pathway Activates Expression of Stress Response Genes by Derepressing the Fos/HDAC Repressor Complex

Ayuna Hattori, Tomoaki Mizuno, Mayuko Akamatsu, Naoki Hisamoto, Kunihiro Matsumoto

PLOS Genetics: published February 21, 2013 | https://doi.org/10.1371/journal.pgen.1003315

Admixture Mapping in Lupus Identifies Multiple Functional Variants within IFIH1 Associated with Apoptosis, Inflammation, and Autoantibody Production

Julio E. Molineros, Amit K. Maiti, Celi Sun, Loren L. Looger, Shizhong Han, Xana Kim-Howard, Stuart Glenn, Adam Adler, Jennifer A. Kelly, Timothy B. Niewold, Gary S. Gilkeson, Elizabeth E. Brown, Graciela S. Alarcón, Jeffrey C. Edberg, Michelle Petri, Rosalind Ramsey-Goldman, John D. Reveille, Luis M. Vilá, Barry I. Freedman, Betty P. Tsao, Lindsey A. Criswell, Chaim O. Jacob, Jason H. Moore, Timothy J. Vyse, Carl L. Langefeld, Joel M. Guthridge, Patrick M. Gaffney, Kathy L. Moser, R. Hal Scofield, Marta E. Alarcón-Riquelme, on behalf of the BIOLUPUS Network, Scott M. Williams, Joan T. Merrill, Judith A. James, Kenneth M. Kaufman, Robert P. Kimberly, John B. Harley, Swapan K. Nath

PLOS Genetics: published February 18, 2013 | https://doi.org/10.1371/journal.pgen.1003222

Hepatocyte Growth Factor, a Determinant of Airspace Homeostasis in the Murine Lung

Carla Calvi, Megan Podowski, Armando Lopez-Mercado, Shana Metzger, Kaori Misono, Alla Malinina, Dustin Dikeman, Hataya Poonyagariyon, Leslie Ynalvez, Roshanak Derakhshandeh, Anne Le, Mark Merchant, Ralph Schwall, Enid R. Neptune

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003228

A Kinome-Wide RNAi Screen in Drosophila Glia Reveals That the RIO Kinases Mediate Cell Proliferation and Survival through TORC2-Akt Signaling in Glioblastoma

Renee D. Read, Tim R. Fenton, German G. Gomez, Jill Wykosky, Scott R. Vandenberg, Ivan Babic, Akio Iwanami, Huijun Yang, Webster K. Cavenee, Paul S. Mischel, Frank B. Furnari, John B. Thomas

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003253

Only One Isoform of Drosophila melanogaster CTP Synthase Forms the Cytoophidium

Ghows Azzam, Ji-Long Liu

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003256

Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade

Zhenxiang Xi, Yuguo Wang, Robert K. Bradley, M. Sugumaran, Christopher J. Marx, Joshua S. Rest, Charles C. Davis

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003265

Expression of a Novel P22 ORFan Gene Reveals the Phage Carrier State in Salmonella Typhimurium

William Cenens, Mehari T. Mebrhatu, Angella Makumi, Pieter-Jan Ceyssens, Rob Lavigne, Rob Van Houdt, François Taddei, Abram Aertsen

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003269

ImmunoChip Study Implicates Antigen Presentation to T Cells in Narcolepsy

Juliette Faraco, Ling Lin, Birgitte Rahbek Kornum, Eimear E. Kenny, Gosia Trynka, Mali Einen, Tom J. Rico, Peter Lichtner, Yves Dauvilliers, Isabelle Arnulf, Michel Lecendreux, Sirous Javidi, Peter Geisler, Geert Mayer, Fabio Pizza, Francesca Poli, Giuseppe Plazzi, Sebastiaan Overeem, Gert Jan Lammers, David Kemlink, Karel Sonka, Sona Nevsimalova, Guy Rouleau, Alex Desautels, Jacques Montplaisir, Birgit Frauscher, Laura Ehrmann, Birgit Högl, Poul Jennum, Patrice Bourgin, Rosa Peraita-Adrados, Alex Iranzo, Claudio Bassetti, Wei-Min Chen, Patrick Concannon, Susan D. Thompson, Vincent Damotte, Bertrand Fontaine, Maxime Breban, Christian Gieger, Norman Klopp, Panos Deloukas, Cisca Wijmenga, Joachim Hallmayer, Suna Onengut-Gumuscu, Stephen S. Rich, Juliane Winkelmann, Emmanuel Mignot

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003270

A Regulatory Pathway, Ecdysone-Transcription Factor Relish-Cathepsin L, Is Involved in Insect Fat Body Dissociation

Yao Zhang, Yu-Xuan Lu, Jian Liu, Cui Yang, Qi-Li Feng, Wei-Hua Xu

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003273

Tysnd1 Deficiency in Mice Interferes with the Peroxisomal Localization of PTS2 Enzymes, Causing Lipid Metabolic Abnormalities and Male Infertility

Yumi Mizuno, Yuichi Ninomiya, Yutaka Nakachi, Mioko Iseki, Hiroyasu Iwasa, Masumi Akita, Tohru Tsukui, Nobuyuki Shimozawa, Chizuru Ito, Kiyotaka Toshimori, Megumi Nishimukai, Hiroshi Hara, Ryouta Maeba, Tomoki Okazaki, Ali Nasser Ali Alodaib, Mohammed Al Amoudi, Minnie Jacob, Fowzan S. Alkuraya, Yasushi Horai, Mitsuhiro Watanabe, Hiromi Motegi, Shigeharu Wakana, Tetsuo Noda, Igor V. Kurochkin, Yosuke Mizuno, Christian Schönbach, Yasushi Okazaki

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003286

miR-199a-5p Is Upregulated during Fibrogenic Response to Tissue Injury and Mediates TGFbeta-Induced Lung Fibroblast Activation by Targeting Caveolin-1

Christian Lacks Lino Cardenas, Imène Sarah Henaoui, Elisabeth Courcot, Christoph Roderburg, Christelle Cauffiez, Sébastien Aubert, Marie-Christine Copin, Benoit Wallaert, François Glowacki, Edmone Dewaeles, Jadranka Milosevic, Julien Maurizio, John Tedrow, Brice Marcet, Jean-Marc Lo-Guidice, Naftali Kaminski, Pascal Barbry, Tom Luedde, Michael Perrais, Bernard Mari, Nicolas Pottier

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003291

Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe

Clio Der Sarkissian, Oleg Balanovsky, Guido Brandt, Valery Khartanovich, Alexandra Buzhilova, Sergey Koshel, Valery Zaporozhchenko, Detlef Gronenborn, Vyacheslav Moiseyev, Eugen Kolpakov, Vladimir Shumkin, Kurt W. Alt, Elena Balanovska, Alan Cooper, Wolfgang Haak, the Genographic Consortium

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003296

The Prefoldin Bud27 Mediates the Assembly of the Eukaryotic RNA Polymerases in an Rpb5-Dependent Manner

María Carmen Mirón-García, Ana Isabel Garrido-Godino, Varinia García-Molinero, Francisco Hernández-Torres, Susana Rodríguez-Navarro, Francisco Navarro

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003297

Identification of the SlmA Active Site Responsible for Blocking Bacterial Cytokinetic Ring Assembly over the Chromosome

Hongbaek Cho, Thomas G. Bernhardt

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003304

The Archipelago Ubiquitin Ligase Subunit Acts in Target Tissue to Restrict Tracheal Terminal Cell Branching and Hypoxic-Induced Gene Expression

Nathan T. Mortimer, Kenneth H. Moberg

PLOS Genetics: published February 14, 2013 | https://doi.org/10.1371/journal.pgen.1003314

The Mub1/Ubr2 Ubiquitin Ligase Complex Regulates the Conserved Dsn1 Kinetochore Protein

Bungo Akiyoshi, Christian R. Nelson, Nicole Duggan, Steven Ceto, Jeffrey A. Ranish, Sue Biggins

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003216

Genetic Landscape of Open Chromatin in Yeast

Kibaick Lee, Sang Cheol Kim, Inkyung Jung, Kwoneel Kim, Jungmin Seo, Heun-Sik Lee, Gireesh K. Bogu, Dongsup Kim, Sanghyuk Lee, Byungwook Lee, Jung Kyoon Choi

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003229

Altered Cohesin Gene Dosage Affects Mammalian Meiotic Chromosome Structure and Behavior

Brenda Murdoch, Nichole Owen, Michelle Stevense, Helen Smith, So Nagaoka, Terry Hassold, Michael McKay, Huiling Xu, Jun Fu, Ekaterina Revenkova, Rolf Jessberger, Patricia Hunt

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003241

Complex Inheritance of Melanoma and Pigmentation of Coat and Skin in Grey Horses

Ino Curik, Thomas Druml, Monika Seltenhammer, Elisabeth Sundström, Gerli Rosengren Pielberg, Leif Andersson, Johann Sölkner

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003248

Assembly of the Auditory Circuitry by a Hox Genetic Network in the Mouse Brainstem

Maria Di Bonito, Yuichi Narita, Bice Avallone, Luigi Sequino, Marta Mancuso, Gennaro Andolfi, Anna Maria Franzè, Luis Puelles, Filippo M. Rijli, Michèle Studer

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003249

DNA–Methylome Analysis of Mouse Intestinal Adenoma Identifies a Tumour-Specific Signature That Is Partly Conserved in Human Colon Cancer

Christina Grimm, Lukas Chavez, Mireia Vilardell, Alexandra L. Farrall, Sascha Tierling, Julia W. Böhm, Phillip Grote, Matthias Lienhard, Jörn Dietrich, Bernd Timmermann, Jörn Walter, Michal R. Schweiger, Hans Lehrach, Ralf Herwig, Bernhard G. Herrmann, Markus Morkel

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003250

Inflammation-Mediated Genetic and Epigenetic Alterations Drive Cancer Development in the Neighboring Epithelium upon Stromal Abrogation of TGF-β Signaling

B. R. Achyut, David A. Bader, Ana I. Robles, Darawalee Wangsa, Curtis C. Harris, Thomas Ried, Li Yang

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003251

Antagonism Versus Cooperativity with TALE Cofactors at the Base of the Functional Diversification of Hox Protein Function

María Luisa Rivas, Jose Manuel Espinosa-Vázquez, Nagraj Sambrani, Stephen Greig, Samir Merabet, Yacine Graba, James Castelli-Gair Hombría

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003252

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

Xi Wang, Detlef Weigel, Lisa M. Smith

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003255

Single Transmembrane Peptide DinQ Modulates Membrane-Dependent Activities

Ragnhild Weel-Sneve, Knut Ivan Kristiansen, Ingvild Odsbu, Bjørn Dalhus, James Booth, Torbjørn Rognes, Kirsten Skarstad, Magnar Bjørås

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003260

Regulation of Drosophila Metamorphosis by Xenobiotic Response Regulators

Huai Deng, Tom K. Kerppola

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003263

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

Xiang Zhou, Peter Carbonetto, Matthew Stephens

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003264

A Meta-Analysis of Thyroid-Related Traits Reveals Novel Loci and Gender-Specific Differences in the Regulation of Thyroid Function

Eleonora Porcu, Marco Medici, Giorgio Pistis, Claudia B. Volpato, Scott G. Wilson, Anne R. Cappola, Steffan D. Bos, Joris Deelen, Martin den Heijer, Rachel M. Freathy, Jari Lahti, Chunyu Liu, Lorna M. Lopez, Ilja M. Nolte, Jeffrey R. O'Connell, Toshiko Tanaka, Stella Trompet, Alice Arnold, Stefania Bandinelli, Marian Beekman, Stefan Böhringer, Suzanne J. Brown, Brendan M. Buckley, Clara Camaschella, Anton J. M. de Craen, Gail Davies, Marieke C. H. de Visser, Ian Ford, Tom Forsen, Timothy M. Frayling, Laura Fugazzola, Martin Gögele, Andrew T. Hattersley, Ad R. Hermus, Albert Hofman, Jeanine J. Houwing-Duistermaat, Richard A. Jensen, Eero Kajantie, Margreet Kloppenburg, Ee M. Lim, Corrado Masciullo, Stefano Mariotti, Cosetta Minelli, Braxton D. Mitchell, Ramaiah Nagaraja, Romana T. Netea-Maier, Aarno Palotie, Luca Persani, Maria G. Piras, Bruce M. Psaty, Katri Räikkönen, J. Brent Richards, Fernando Rivadeneira, Cinzia Sala, Mona M. Sabra, Naveed Sattar, Beverley M. Shields, Nicole Soranzo, John M. Starr, David J. Stott, Fred C. G. J. Sweep, Gianluca Usala, Melanie M. van der Klauw, Diana van Heemst, Alies van Mullem, Sita H.Vermeulen, W. Edward Visser, John P. Walsh, Rudi G. J. Westendorp, Elisabeth Widen, Guangju Zhai, Francesco Cucca, Ian J. Deary, Johan G. Eriksson, Luigi Ferrucci, Caroline S. Fox, J. Wouter Jukema, Lambertus A. Kiemeney, Peter P. Pramstaller, David Schlessinger, Alan R. Shuldiner, Eline P. Slagboom, André G. Uitterlinden, Bijay Vaidya, Theo J. Visser, Bruce H. R. Wolffenbuttel, Ingrid Meulenbelt, Jerome I. Rotter, Tim D. Spector, Andrew A. Hicks, Daniela Toniolo, Serena Sanna, Robin P. Peeters, Silvia Naitza

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003266

DNA Methylation Mediated Control of Gene Expression Is Critical for Development of Crown Gall Tumors

Jochen Gohlke, Claus-Juergen Scholz, Susanne Kneitz, Dana Weber, Joerg Fuchs, Rainer Hedrich, Rosalia Deeken

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003267

Control of Multicellular Development by the Physically Interacting Deneddylases DEN1/DenA and COP9 Signalosome

Martin Christmann, Tilo Schmaler, Colin Gordon, Xiaohua Huang, Özgür Bayram, Josua Schinke, Sina Stumpf, Wolfgang Dubiel, Gerhard H. Braus

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003275

COM-1 Promotes Homologous Recombination during Caenorhabditis elegans Meiosis by Antagonizing Ku-Mediated Non-Homologous End Joining

Bennie B. L. G. Lemmens, Nicholas M. Johnson, Marcel Tijsterman

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003276

Regulation of Neurod1 Contributes to the Lineage Potential of Neurogenin3+ Endocrine Precursor Cells in the Pancreas

Teresa L. Mastracci, Keith R. Anderson, James B. Papizan, Lori Sussel

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003278

Autophagy Induction Is a Tor- and Tp53-Independent Cell Survival Response in a Zebrafish Model of Disrupted Ribosome Biogenesis

Yeliz Boglev, Andrew P. Badrock, Andrew J. Trotter, Qian Du, Elsbeth J. Richardson, Adam C. Parslow, Sebastian J. Markmiller, Nathan E. Hall, Tanya A. de Jong-Curtain, Annie Y. Ng, Heather Verkade, Elke A. Ober, Holly A. Field, Donghun Shin, Chong H. Shin, Katherine M. Hannan, Ross D. Hannan, Richard B. Pearson, Seok-Hyung Kim, Kevin C. Ess, Graham J. Lieschke, Didier Y. R. Stainier, Joan K. Heath

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003279

Drosophila Yemanuclein and HIRA Cooperate for De Novo Assembly of H3.3-Containing Nucleosomes in the Male Pronucleus

Guillermo A. Orsi, Ahmed Algazeery, Régis E. Meyer, Michèle Capri, Laure M. Sapey-Triomphe, Béatrice Horard, Henri Gruffat, Pierre Couble, Ounissa Aït-Ahmed, Benjamin Loppin

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003285

Duplicate Abalone Egg Coat Proteins Bind Sperm Lysin Similarly, but Evolve Oppositely, Consistent with Molecular Mimicry at Fertilization

Jan E. Aagaard, Stevan A. Springer, Scott D. Soelberg, Willie J. Swanson

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003287

Mitotic Evolution of Plasmodium falciparum Shows a Stable Core Genome but Recombination in Antigen Families

Selina E. R. Bopp, Micah J. Manary, A. Taylor Bright, Geoffrey L. Johnston, Neekesh V. Dharia, Fabio L. Luna, Susan McCormack, David Plouffe, Case W. McNamara, John R. Walker, David A. Fidock, Eros Lazzerini Denchi, Elizabeth A. Winzeler

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003293

Essential Developmental, Genomic Stability, and Tumour Suppressor Functions of the Mouse Orthologue of hSSB1/NABP2

Wei Shi, Amanda L. Bain, Bjoern Schwer, Fares Al-Ejeh, Corey Smith, Lee Wong, Hua Chai, Mariska S. Miranda, Uda Ho, Makoto Kawaguchi, Yutaka Miura, John W. Finnie, Meaghan Wall, Jörg Heierhorst, Carol Wicking, Kevin J. Spring, Frederick W. Alt, Kum Kum Khanna

PLOS Genetics: published February 7, 2013 | https://doi.org/10.1371/journal.pgen.1003298

RNAi–Based Functional Profiling of Loci from Blood Lipid Genome-Wide Association Studies Identifies Genes with Cholesterol-Regulatory Function

Peter Blattmann, Christian Schuberth, Rainer Pepperkok, Heiko Runz

PLOS Genetics: published February 28, 2013 | https://doi.org/10.1371/journal.pgen.1003338

Cover

Modifying the modifier: polymorphic variants of the mismatch repair protein MSH3 modify disease-causing CAG/CTG repeat expansions.

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