October 2012

Mendel established that heterozygous alleles typically segregate in a 2:2 ratio during meiosis. The molecular events that accompany meiotic recombination can also cause a nonreciprocal exchange of information between parental chromosomes that results in a non-Mendelian 3:1 segregation pattern called gene conversion. In this issue, Sun et al. use a visual, pollen tetrad–based assay to measure the frequency of gene conversion across the genome of the model plant Arabidopsis thaliana.

Image Credit: Yujin Sun and Gregory P. Copenhaver (The University of North Carolina at Chapel Hill).

Interview

It Was Heaven: An Interview with Evelyn Witkin

Jane Gitschier

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1003009

Perspective

Classical Genetics Meets Next-Generation Sequencing: Uncovering a Genome-Wide Recombination Map in Drosophila melanogaster

Nadia D. Singh

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1003024

Research Articles

Topoisomerase II– and Condensin-Dependent Breakage of MEC1^ATR-Sensitive Fragile Sites Occurs Independently of Spindle Tension, Anaphase, or Cytokinesis

Nadia Hashash, Anthony L. Johnson, Rita S. Cha

PLOS Genetics: published October 25, 2012 | https://doi.org/10.1371/journal.pgen.1002978

Variants Affecting Exon Skipping Contribute to Complex Traits

Younghee Lee, Eric R. Gamazon, Ellen Rebman, Yeunsook Lee, Sanghyuk Lee, M. Eileen Dolan, Nancy J. Cox, Yves A. Lussier

PLOS Genetics: published October 25, 2012 | https://doi.org/10.1371/journal.pgen.1002998

Comparative Genomics Suggests an Independent Origin of Cytoplasmic Incompatibility in Cardinium hertigii

Thomas Penz, Stephan Schmitz-Esser, Suzanne E. Kelly, Bodil N. Cass, Anneliese Müller, Tanja Woyke, Stephanie A. Malfatti, Martha S. Hunter, Matthias Horn

PLOS Genetics: published October 25, 2012 | https://doi.org/10.1371/journal.pgen.1003012

Morphogenesis and Cell Fate Determination within the Adaxial Cell Equivalence Group of the Zebrafish Myotome

Mai E. Nguyen-Chi, Robert Bryson-Richardson, Carmen Sonntag, Thomas E. Hall, Abigail Gibson, Tamar Sztal, Wendy Chua, Thomas F. Schilling, Peter D. Currie

PLOS Genetics: published October 25, 2012 | https://doi.org/10.1371/journal.pgen.1003014

Embryos of Robertsonian Translocation Carriers Exhibit a Mitotic Interchromosomal Effect That Enhances Genetic Instability during Early Development

Samer Alfarawati, Elpida Fragouli, Pere Colls, Dagan Wells

PLOS Genetics: published October 25, 2012 | https://doi.org/10.1371/journal.pgen.1003025

MOV10 RNA Helicase Is a Potent Inhibitor of Retrotransposition in Cells

John L. Goodier, Ling E. Cheung, Haig H. Kazazian Jr.

PLOS Genetics: published October 18, 2012 | https://doi.org/10.1371/journal.pgen.1002941

Recovery of Arrested Replication Forks by Homologous Recombination Is Error-Prone

Ismail Iraqui, Yasmina Chekkal, Nada Jmari, Violena Pietrobon, Karine Fréon, Audrey Costes, Sarah A. E. Lambert

PLOS Genetics: published October 18, 2012 | https://doi.org/10.1371/journal.pgen.1002976

Cytokinesis-Based Constraints on Polarized Cell Growth in Fission Yeast

K. Adam Bohnert, Kathleen L. Gould

PLOS Genetics: published October 18, 2012 | https://doi.org/10.1371/journal.pgen.1003004

Mining the Unknown: A Systems Approach to Metabolite Identification Combining Genetic and Metabolic Information

Jan Krumsiek, Karsten Suhre, Anne M. Evans, Matthew W. Mitchell, Robert P. Mohney, Michael V. Milburn, Brigitte Wägele, Werner Römisch-Margl, Thomas Illig, Jerzy Adamski, Christian Gieger, Fabian J. Theis, Gabi Kastenmüller

PLOS Genetics: published October 18, 2012 | https://doi.org/10.1371/journal.pgen.1003005

Regulation of ATG4B Stability by RNF5 Limits Basal Levels of Autophagy and Influences Susceptibility to Bacterial Infection

Ersheng Kuang, Cheryl Y. M. Okumura, Sharon Sheffy-Levin, Tal Varsano, Vincent Chih-Wen Shu, Jianfei Qi, Ingrid R. Niesman, Huei-Jiun Yang, Carlos López-Otín, Wei Yuan Yang, John C. Reed, Limor Broday, Victor Nizet, Ze'ev A. Ronai

PLOS Genetics: published October 18, 2012 | https://doi.org/10.1371/journal.pgen.1003007

Specific Missense Alleles of the Arabidopsis Jasmonic Acid Co-Receptor COI1 Regulate Innate Immune Receptor Accumulation and Function

Yijian He, Eui-Hwan Chung, David A. Hubert, Pablo Tornero, Jeffery L. Dangl

PLOS Genetics: published October 18, 2012 | https://doi.org/10.1371/journal.pgen.1003018

Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism

Tim R. Blower, Terry J. Evans, Rita Przybilski, Peter C. Fineran, George P. C. Salmond

PLOS Genetics: published October 18, 2012 | https://doi.org/10.1371/journal.pgen.1003023

The Many Landscapes of Recombination in Drosophila melanogaster

Josep M. Comeron, Ramesh Ratnappan, Samuel Bailin

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002905

Increasing Signal Specificity of the TOL Network of Pseudomonas putida mt-2 by Rewiring the Connectivity of the Master Regulator XylR

Aitor de las Heras, Sofia Fraile, Victor de Lorenzo

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002963

Phosphatase-Dead Myotubularin Ameliorates X-Linked Centronuclear Myopathy Phenotypes in Mice

Leonela Amoasii, Dimitri L. Bertazzi, Hélène Tronchère, Karim Hnia, Gaëtan Chicanne, Bruno Rinaldi, Belinda S. Cowling, Arnaud Ferry, Bruno Klaholz, Bernard Payrastre, Jocelyn Laporte, Sylvie Friant

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002965

Loss of Slc4a1b Chloride/Bicarbonate Exchanger Function Protects Mechanosensory Hair Cells from Aminoglycoside Damage in the Zebrafish Mutant persephone

Dale W. Hailey, Brock Roberts, Kelly N. Owens, Andrew K. Stewart, Tor Linbo, Remy Pujol, Seth L. Alper, Edwin W. Rubel, David W. Raible

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002971

Comparison of Family History and SNPs for Predicting Risk of Complex Disease

Chuong B. Do, David A. Hinds, Uta Francke, Nicholas Eriksson

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002973

Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes

Devin Coleman-Derr, Daniel Zilberman

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002988

Muscle-Specific Splicing Factors ASD-2 and SUP-12 Cooperatively Switch Alternative Pre-mRNA Processing Patterns of the ADF/Cofilin Gene in Caenorhabditis elegans

Genta Ohno, Kanako Ono, Marina Togo, Yohei Watanabe, Shoichiro Ono, Masatoshi Hagiwara, Hidehito Kuroyanagi

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002991

Full-Length Synaptonemal Complex Grows Continuously during Meiotic Prophase in Budding Yeast

Karen Voelkel-Meiman, Sarah S. Moustafa, Philippe Lefrançois, Anne M. Villeneuve, Amy J. MacQueen

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002993

The SET-Domain Protein SUVR5 Mediates H3K9me2 Deposition and Silencing at Stimulus Response Genes in a DNA Methylation–Independent Manner

Elena Caro, Hume Stroud, Maxim V. C. Greenberg, Yana V. Bernatavichute, Suhua Feng, Martin Groth, Ajay A. Vashisht, James Wohlschlegel, Steve E. Jacobsen

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002995

Cdon Mutation and Fetal Ethanol Exposure Synergize to Produce Midline Signaling Defects and Holoprosencephaly Spectrum Disorders in Mice

Mingi Hong, Robert S. Krauss

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1002999

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels

Athma A. Pai, Carolyn E. Cain, Orna Mizrahi-Man, Sherryl De Leon, Noah Lewellen, Jean-Baptiste Veyrieras, Jacob F. Degner, Daniel J. Gaffney, Joseph K. Pickrell, Matthew Stephens, Jonathan K. Pritchard, Yoav Gilad

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1003000

New Partners in Regulation of Gene Expression: The Enhancer of Trithorax and Polycomb Corto Interacts with Methylated Ribosomal Protein L12 Via Its Chromodomain

Anne Coléno-Costes, Suk Min Jang, Augustin de Vanssay, Julien Rougeot, Tahar Bouceba, Neel B. Randsholt, Jean-Michel Gibert, Stéphane Le Crom, Emmanuèle Mouchel-Vielh, Sébastien Bloyer, Frédérique Peronnet

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1003006

Use of Pleiotropy to Model Genetic Interactions in a Population

Gregory W. Carter, Michelle Hays, Amir Sherman, Timothy Galitski

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1003010

Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation

Benjamin M. Peter, Emilia Huerta-Sanchez, Rasmus Nielsen

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1003011

Faster-X Evolution of Gene Expression in Drosophila

Richard P. Meisel, John H. Malone, Andrew G. Clark

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1003013

Mismatch Repair Balances Leading and Lagging Strand DNA Replication Fidelity

Scott A. Lujan, Jessica S. Williams, Zachary F. Pursell, Amy A. Abdulovic-Cui, Alan B. Clark, Stephanie A. Nick McElhinny, Thomas A. Kunkel

PLOS Genetics: published October 11, 2012 | https://doi.org/10.1371/journal.pgen.1003016

Mutations in Hedgehog Acyltransferase (Hhat) Perturb Hedgehog Signaling, Resulting in Severe Acrania-Holoprosencephaly-Agnathia Craniofacial Defects

Jennifer F. Dennis, Hiroshi Kurosaka, Angelo Iulianella, Jennifer Pace, Nancy Thomas, Sharon Beckham, Trevor Williams, Paul A. Trainor

PLOS Genetics: published October 4, 2012 | https://doi.org/10.1371/journal.pgen.1002927

A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families

Bingshan Li, Wei Chen, Xiaowei Zhan, Fabio Busonero, Serena Sanna, Carlo Sidore, Francesco Cucca, Hyun M. Kang, Gonçalo R. Abecasis

PLOS Genetics: published October 4, 2012 | https://doi.org/10.1371/journal.pgen.1002944

The Date of Interbreeding between Neandertals and Modern Humans

Sriram Sankararaman, Nick Patterson, Heng Li, Svante Pääbo, David Reich

PLOS Genetics: published October 4, 2012 | https://doi.org/10.1371/journal.pgen.1002947

A Mutation in the Srrm4 Gene Causes Alternative Splicing Defects and Deafness in the Bronx Waltzer Mouse

Yoko Nakano, Israt Jahan, Gregory Bonde, Xingshen Sun, Michael S. Hildebrand, John F. Engelhardt, Richard J. H. Smith, Robert A. Cornell, Bernd Fritzsch, Botond Bánfi

PLOS Genetics: published October 4, 2012 | https://doi.org/10.1371/journal.pgen.1002966

Deep Genome-Wide Measurement of Meiotic Gene Conversion Using Tetrad Analysis in Arabidopsis thaliana

Yujin Sun, Jonathan H. Ambrose, Brena S. Haughey, Tyler D. Webster, Sarah N. Pierrie, Daniela F. Muñoz, Emily C. Wellman, Shalom Cherian, Scott M. Lewis, Luke E. Berchowitz, Gregory P. Copenhaver

PLOS Genetics: published October 4, 2012 | https://doi.org/10.1371/journal.pgen.1002968

RAB-Like 2 Has an Essential Role in Male Fertility, Sperm Intra-Flagellar Transport, and Tail Assembly

Jennifer C. Y. Lo, Duangporn Jamsai, Anne E. O'Connor, Claire Borg, Brett J. Clark, James C. Whisstock, Mark C. Field, Vicki Adams, Tomomoto Ishikawa, R. John Aitken, Belinda Whittle, Christopher C. Goodnow, Christopher J. Ormandy, Moira K. O'Bryan

PLOS Genetics: published October 4, 2012 | https://doi.org/10.1371/journal.pgen.1002969

Cofilin-1: A Modulator of Anxiety in Mice

Martin Goodson, Marco B. Rust, Walter Witke, David Bannerman, Richard Mott, Chris P. Ponting, Jonathan Flint

PLOS Genetics: published October 4, 2012 | https://doi.org/10.1371/journal.pgen.1002970

Maize Unstable factor for orange1 Is Required for Maintaining Silencing Associated with Paramutation at the pericarp color1 and booster1 Loci

Rajandeep S. Sekhon, Po-Hao Wang, Lyudmila Sidorenko, Vicki L. Chandler, Surinder Chopra

PLOS Genetics: published October 4, 2012 | https://doi.org/10.1371/journal.pgen.1002980

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences

Olivier Arnaiz, Nathalie Mathy, Céline Baudry, Sophie Malinsky, Jean-Marc Aury, Cyril Denby Wilkes, Olivier Garnier, Karine Labadie, Benjamin E. Lauderdale, Anne Le Mouël, Antoine Marmignon, Mariusz Nowacki, Julie Poulain, Malgorzata Prajer, Patrick Wincker, Eric Meyer, Sandra Duharcourt, Laurent Duret, Mireille Bétermier, Linda Sperling

PLOS Genetics: published October 4, 2012 | https://doi.org/10.1371/journal.pgen.1002984

Cover

Gene conversion in Arabidopsis tetrads.

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**Gene conversion in Arabidopsis tetrads.**