December 2010

Aspergillus nidulans is a cosmopolitan mold growing with filaments (yellow). During the sexual cycle, two fungal partners form closed fruiting bodies (purple), which are covered by hundreds of globose Hülle cells (brown). In this issue of PLoS Genetics, Bayram et al. show that, in the absence of the regulator LaeA, the number of Hülle cells is drastically reduced and results in the shown small fruiting bodies of only 20% of the normal size. This supports the view that nursing the young fruiting body is a major function of Hülle cells.

Image Credit: Özgür Bayram and Gerhard Braus

Perspective

Linking Crohn's Disease and Ankylosing Spondylitis: It's All about Genes!

Dirk Elewaut

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001223

Review

Cancer and Neurodegeneration: Between the Devil and the Deep Blue Sea

Hélène Plun-Favreau, Patrick A. Lewis, John Hardy, L. Miguel Martins, Nicholas W. Wood

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001257

Research Articles

Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

Eva H. Stukenbrock, Frank G. Jørgensen, Marcello Zala, Troels T. Hansen, Bruce A. McDonald, Mikkel H. Schierup

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001189

MOS11: A New Component in the mRNA Export Pathway

Hugo Germain, Na Qu, Yu Ti Cheng, EunKyoung Lee, Yan Huang, Oliver Xiaoou Dong, Patrick Gannon, Shuai Huang, Pingtao Ding, Yingzhong Li, Fred Sack, Yuelin Zhang, Xin Li

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001250

Thymus-Associated Parathyroid Hormone Has Two Cellular Origins with Distinct Endocrine and Immunological Functions

Zhijie Liu, Alison Farley, Lizhen Chen, Beth J. Kirby, Christopher S. Kovacs, C. Clare Blackburn, Nancy R. Manley

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001251

Season of Conception in Rural Gambia Affects DNA Methylation at Putative Human Metastable Epialleles

Robert A. Waterland, Richard Kellermayer, Eleonora Laritsky, Pura Rayco-Solon, R. Alan Harris, Michael Travisano, Wenjuan Zhang, Maria S. Torskaya, Jiexin Zhang, Lanlan Shen, Mark J. Manary, Andrew M. Prentice

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001252

Cleavage of Phosphorothioated DNA and Methylated DNA by the Type IV Restriction Endonuclease ScoMcrA

Guang Liu, Hong-Yu Ou, Tao Wang, Li Li, Huarong Tan, Xiufen Zhou, Kumar Rajakumar, Zixin Deng, Xinyi He

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001253

Identification of Genes Required for Neural-Specific Glycosylation Using Functional Genomics

Miki Yamamoto-Hino, Yoshimi Kanie, Wakae Awano, Kiyoko F. Aoki-Kinoshita, Hiroyuki Yano, Shoko Nishihara, Hideyuki Okano, Ryu Ueda, Osamu Kanie, Satoshi Goto

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001254

A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y-Linked Male Fertility Genes

Yun Ding, Li Zhao, Shuang Yang, Yu Jiang, Yuan Chen, Ruoping Zhao, Yue Zhang, Guojie Zhang, Yang Dong, Haijing Yu, Qi Zhou, Wen Wang

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001255

Genomics Meets Glycomics—The First GWAS Study of Human N-Glycome Identifies HNF1α as a Master Regulator of Plasma Protein Fucosylation

Gordan Lauc, Abdelkader Essafi, Jennifer E. Huffman, Caroline Hayward, Ana Knežević, Jayesh J. Kattla, Ozren Polašek, Olga Gornik, Veronique Vitart, Jodie L. Abrahams, Maja Pučić, Mislav Novokmet, Irma Redžić, Susan Campbell, Sarah H. Wild, Fran Borovečki, Wei Wang, Ivana Kolčić, Lina Zgaga, Ulf Gyllensten, James F. Wilson, Alan F. Wright, Nicholas D. Hastie, Harry Campbell, Pauline M. Rudd, Igor Rudan

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001256

A Role for ATF2 in Regulating MITF and Melanoma Development

Meera Shah, Anindita Bhoumik, Vikas Goel, Antimone Dewing, Wolfgang Breitwieser, Harriet Kluger, Stan Krajewski, Maryla Krajewska, Jason DeHart, Eric Lau, David M. Kallenberg, Hyeongnam Jeong, Alexey Eroshkin, Dorothy C. Bennett, Lynda Chin, Marcus Bosenberg, Nic Jones, Ze'ev A. Ronai

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001258

Ancestral Regulatory Circuits Governing Ectoderm Patterning Downstream of Nodal and BMP2/4 Revealed by Gene Regulatory Network Analysis in an Echinoderm

Alexandra Saudemont, Emmanuel Haillot, Flavien Mekpoh, Nathalie Bessodes, Magali Quirin, François Lapraz, Véronique Duboc, Eric Röttinger, Ryan Range, Arnaud Oisel, Lydia Besnardeau, Patrick Wincker, Thierry Lepage

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001259

Initiator Elements Function to Determine the Activity State of BX-C Enhancers

Carole Iampietro, Maheshwar Gummalla, Annick Mutero, François Karch, Robert K. Maeda

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001260

Self-Mating in the Definitive Host Potentiates Clonal Outbreaks of the Apicomplexan Parasites Sarcocystis neurona and Toxoplasma gondii

Jered M. Wendte, Melissa A. Miller, Dyanna M. Lambourn, Spencer L. Magargal, David A. Jessup, Michael E. Grigg

PLOS Genetics: published December 23, 2010 | https://doi.org/10.1371/journal.pgen.1001261

A Single Enhancer Regulating the Differential Expression of Duplicated Red-Sensitive Opsin Genes in Zebrafish

Taro Tsujimura, Tomohiro Hosoya, Shoji Kawamura

PLOS Genetics: published December 16, 2010 | https://doi.org/10.1371/journal.pgen.1001245

Distinct Functions for the Drosophila piRNA Pathway in Genome Maintenance and Telomere Protection

Jaspreet S. Khurana, Jia Xu, Zhiping Weng, William E. Theurkauf

PLOS Genetics: published December 16, 2010 | https://doi.org/10.1371/journal.pgen.1001246

A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress

Clement T. Y. Chan, Madhu Dyavaiah, Michael S. DeMott, Koli Taghizadeh, Peter C. Dedon, Thomas J. Begley

PLOS Genetics: published December 16, 2010 | https://doi.org/10.1371/journal.pgen.1001247

An ABC Transporter Mutation Is Correlated with Insect Resistance to Bacillus thuringiensis Cry1Ac Toxin

Linda J. Gahan, Yannick Pauchet, Heiko Vogel, David G. Heckel

PLOS Genetics: published December 16, 2010 | https://doi.org/10.1371/journal.pgen.1001248

Functional Comparison of Innate Immune Signaling Pathways in Primates

Luis B. Barreiro, John C. Marioni, Ran Blekhman, Matthew Stephens, Yoav Gilad

PLOS Genetics: published December 16, 2010 | https://doi.org/10.1371/journal.pgen.1001249

Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding

Christine Vogler, Claudia Huber, Tanja Waldmann, Ramona Ettig, Lora Braun, Annalisa Izzo, Sylvain Daujat, Isabelle Chassignet, Andres Joaquin Lopez-Contreras, Oscar Fernandez-Capetillo, Miroslav Dundr, Karsten Rippe, Gernot Längst, Robert Schneider

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001234

Endocytic Sorting and Recycling Require Membrane Phosphatidylserine Asymmetry Maintained by TAT-1/CHAT-1

Baohui Chen, Yue Jiang, Sheng Zeng, Jiacong Yan, Xin Li, Yan Zhang, Wei Zou, Xiaochen Wang

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001235

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

Joseph K. Pickrell, Athma A. Pai, Yoav Gilad, Jonathan K. Pritchard

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001236

Reduction of Protein Translation and Activation of Autophagy Protect against PINK1 Pathogenesis in Drosophila melanogaster

Song Liu, Bingwei Lu

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001237

The C-Terminal Domain of the Bacterial SSB Protein Acts as a DNA Maintenance Hub at Active Chromosome Replication Forks

Audrey Costes, François Lecointe, Stephen McGovern, Sophie Quevillon-Cheruel, Patrice Polard

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001238

Investigation and Functional Characterization of Rare Genetic Variants in the Adipose Triglyceride Lipase in a Large Healthy Working Population

Stefan Coassin, Martina Schweiger, Anita Kloss-Brandstätter, Claudia Lamina, Margot Haun, Gertraud Erhart, Bernhard Paulweber, Yusof Rahman, Simon Olpin, Heimo Wolinski, Irina Cornaciu, Rudolf Zechner, Robert Zimmermann, Florian Kronenberg

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001239

Histone Deacetylases Suppress CGG Repeat–Induced Neurodegeneration Via Transcriptional Silencing in Models of Fragile X Tremor Ataxia Syndrome

Peter K. Todd, Seok Yoon Oh, Amy Krans, Udai B. Pandey, Nicholas A. Di Prospero, Kyung-Tai Min, J. Paul Taylor, Henry L. Paulson

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001240

Genome-Wide Interrogation of Mammalian Stem Cell Fate Determinants by Nested Chromosome Deletions

Simon Fortier, Mélanie Bilodeau, Tara MacRae, Jean-Philippe Laverdure, Valeria Azcoitia, Simon Girard, Jalila Chagraoui, Nancy Ringuette, Josée Hébert, Jana Krosl, Nadine Mayotte, Guy Sauvageau

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001241

Continuous and Periodic Expansion of CAG Repeats in Huntington's Disease R6/1 Mice

Linda Møllersen, Alexander D. Rowe, Elisabeth Larsen, Torbjørn Rognes, Arne Klungland

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001242

The EpsE Flagellar Clutch Is Bifunctional and Synergizes with EPS Biosynthesis to Promote Bacillus subtilis Biofilm Formation

Sarah B. Guttenplan, Kris M. Blair, Daniel B. Kearns

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001243

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

Eric M. Mendenhall, Richard P. Koche, Thanh Truong, Vicky W. Zhou, Biju Issac, Andrew S. Chi, Manching Ku, Bradley E. Bernstein

PLOS Genetics: published December 9, 2010 | https://doi.org/10.1371/journal.pgen.1001244

Association of Variants at 1q32 and STAT3 with Ankylosing Spondylitis Suggests Genetic Overlap with Crohn's Disease

Patrick Danoy, Karena Pryce, Johanna Hadler, Linda A. Bradbury, Claire Farrar, Jennifer Pointon, Australo-Anglo-American Spondyloarthritis Consortium (TASC), Michael Ward, Michael Weisman, John D. Reveille, B. Paul Wordsworth, Millicent A. Stone, Spondyloarthritis Research Consortium of Canada (SPARCC), Walter P. Maksymowych, Proton Rahman, Dafna Gladman, Robert D. Inman, Matthew A. Brown

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001195

LaeA Control of Velvet Family Regulatory Proteins for Light-Dependent Development and Fungal Cell-Type Specificity

Özlem Sarikaya Bayram, Özgür Bayram, Oliver Valerius, Hee Soo Park, Stefan Irniger, Jennifer Gerke, Min Ni, Kap-Hoon Han, Jae-Hyuk Yu, Gerhard H. Braus

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001226

The DNA Damage Response Pathway Contributes to the Stability of Chromosome III Derivatives Lacking Efficient Replicators

James F. Theis, Carmela Irene, Ann Dershowitz, Renee L. Brost, Michael L. Tobin, Fabiana M. di Sanzo, Jian-Ying Wang, Charles Boone, Carol S. Newlon

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001227

Competitive Repair by Naturally Dispersed Repetitive DNA during Non-Allelic Homologous Recombination

Margaret L. Hoang, Frederick J. Tan, David C. Lai, Sue E. Celniker, Roger A. Hoskins, Maitreya J. Dunham, Yixian Zheng, Douglas Koshland

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001228

The Loss of PGAM5 Suppresses the Mitochondrial Degeneration Caused by Inactivation of PINK1 in Drosophila

Yuzuru Imai, Tomoko Kanao, Tomoyo Sawada, Yoshito Kobayashi, Yasuhiro Moriwaki, Yosuke Ishida, Kohsuke Takeda, Hidenori Ichijo, Bingwei Lu, Ryosuke Takahashi

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001229

A Unifying Framework for Evaluating the Predictive Power of Genetic Variants Based on the Level of Heritability Explained

Hon-Cheong So, Pak C. Sham

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001230

Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells

Karsten Jürchott, Ralf-Jürgen Kuban, Till Krech, Nils Blüthgen, Ulrike Stein, Wolfgang Walther, Christian Friese, Szymon M. Kiełbasa, Ute Ungethüm, Per Lund, Thomas Knösel, Wolfgang Kemmner, Markus Morkel, Johannes Fritzmann, Peter M. Schlag, Walter Birchmeier, Tammo Krueger, Silke Sperling, Christine Sers, Hans-Dieter Royer, Hanspeter Herzel, Reinhold Schäfer

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001231

Role of Individual Subunits of the Neurospora crassa CSN Complex in Regulation of Deneddylation and Stability of Cullin Proteins

Jiyong Wang, Qiwen Hu, Huijie Chen, Zhipeng Zhou, Weihua Li, Ying Wang, Shaojie Li, Qun He

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001232

Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk

Christin E. Burd, William R. Jeck, Yan Liu, Hanna K. Sanoff, Zefeng Wang, Norman E. Sharpless

PLOS Genetics: published December 2, 2010 | https://doi.org/10.1371/journal.pgen.1001233

Cover

A mutant fungal fruiting body.

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