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Table of Contents

November 2009

Cover

Maize plant demonstrating the anther pigment phenotype of a mutation that prevents paramutation, a heritable RNA-mediated gene-silencing process.
Issue Image

Research Articles by Sidorenko et al. and Stonaker et al. in this issue of PLoS Genetics demonstrate that mutations in NRPD2/E2a similar to Arabidopsis NRPD2/E2, the second largest subunit of plant-specific RNA polymerases IV and V, prevent paramutation at multiple loci. In contrast to the single gene in Arabidopsis, maize has three full-length genes with overlapping expression patterns, suggesting maize may have a greater diversification of these gene-silencing pathways. Craig Pikaard's Perspective highlights key findings and open questions. These articles coincide with the publication of the 2009 Maize Genome Collection, which is based on the first description of the B73 maize genome.

Image Credit: Lyudmila Sidorenko (School of Plant Sciences, Bio5, University of Arizona, United States of America)

Editorial

10 Reasons to be Tantalized by the B73 Maize Genome

Virginia Walbot

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000723

Perspectives

X Chromosome: Expression and Escape

John Parsch

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000724

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  1. Stage-Specific Expression Profiling of Drosophila Spermatogenesis Suggests that Meiotic Sex Chromosome Inactivation Drives Genomic Relocation of Testis-Expressed Genes

RNA-Silencing Enzymes Pol IV and Pol V in Maize: More than one Flavor?

Craig S. Pikaard, Sarah Tucker

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000736

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  1. A Dominant Mutation in mediator of paramutation2, One of Three Second-Largest Subunits of a Plant-Specific RNA Polymerase, Disrupts Multiple siRNA Silencing Processes
  2. Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 Locus

Research Articles

Identification of Positive Regulators of the Yeast Fps1 Glycerol Channel

Sara E. Beese, Takahiro Negishi, David E. Levin

PLOS Genetics: published November 26, 2009 | https://doi.org/10.1371/journal.pgen.1000738

Cohesin Is Required for Higher-Order Chromatin Conformation at the Imprinted IGF2-H19 Locus

Raffaella Nativio, Kerstin S. Wendt, Yoko Ito, Joanna E. Huddleston, Santiago Uribe-Lewis, Kathryn Woodfine, Christel Krueger, Wolf Reik, Jan-Michael Peters, Adele Murrell

PLOS Genetics: published November 26, 2009 | https://doi.org/10.1371/journal.pgen.1000739

On the Analysis of Genome-Wide Association Studies in Family-Based Designs: A Universal, Robust Analysis Approach and an Application to Four Genome-Wide Association Studies

Sungho Won, Jemma B. Wilk, Rasika A. Mathias, Christopher J. O'Donnell, Edwin K. Silverman, Kathleen Barnes, George T. O'Connor, Scott T. Weiss, Christoph Lange

PLOS Genetics: published November 26, 2009 | https://doi.org/10.1371/journal.pgen.1000741

The Fitness Effects of Random Mutations in Single-Stranded DNA and RNA Bacteriophages

Pilar Domingo-Calap, José M. Cuevas, Rafael Sanjuán

PLOS Genetics: published November 26, 2009 | https://doi.org/10.1371/journal.pgen.1000742

Basonuclin-2 Requirements for Zebrafish Adult Pigment Pattern Development and Female Fertility

Michael R. Lang, Larissa B. Patterson, Tiffany N. Gordon, Stephen L. Johnson, David M. Parichy

PLOS Genetics: published November 26, 2009 | https://doi.org/10.1371/journal.pgen.1000744

Frequent Long-Range Epigenetic Silencing of Protocadherin Gene Clusters on Chromosome 5q31 in Wilms' Tumor

Anthony R. Dallosso, Anne L. Hancock, Marianna Szemes, Kim Moorwood, Laxmi Chilukamarri, Hsin-Hao Tsai, Abby Sarkar, Jonathan Barasch, Raisa Vuononvirta, Chris Jones, Kathy Pritchard-Jones, Brigitte Royer-Pokora, Sean Bong Lee, Ceris Owen, Sally Malik, Yi Feng, Marcus Frank, Andrew Ward, Keith W. Brown, Karim Malik

PLOS Genetics: published November 26, 2009 | https://doi.org/10.1371/journal.pgen.1000745

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  1. Correction: Frequent Long-Range Epigenetic Silencing of Protocadherin Gene Clusters on Chromosome 5q31 in Wilms' Tumor

Serrano (Sano) Functions with the Planar Cell Polarity Genes to Control Tracheal Tube Length

SeYeon Chung, Melissa S. Vining, Pamela L. Bradley, Chih-Chiang Chan, Keith A. Wharton Jr, Deborah J. Andrew

PLOS Genetics: published November 26, 2009 | https://doi.org/10.1371/journal.pgen.1000746

Mutations in GDF5 Reveal a Key Residue Mediating BMP Inhibition by NOGGIN

Petra Seemann, Anja Brehm, Jana König, Carsten Reissner, Sigmar Stricker, Pia Kuss, Julia Haupt, Stephanie Renninger, Joachim Nickel, Walter Sebald, Jay C. Groppe, Frank Plöger, Jens Pohl, Mareen Schmidt-von Kegler, Maria Walther, Ingmar Gassner, Cristina Rusu, Andreas R. Janecke, Katarina Dathe, Stefan Mundlos

PLOS Genetics: published November 26, 2009 | https://doi.org/10.1371/journal.pgen.1000747

Palmitoylation Regulates Epidermal Homeostasis and Hair Follicle Differentiation

Pleasantine Mill, Angela W. S. Lee, Yuko Fukata, Ryouhei Tsutsumi, Masaki Fukata, Margaret Keighren, Rebecca M. Porter, Lisa McKie, Ian Smyth, Ian J. Jackson

PLOS Genetics: published November 26, 2009 | https://doi.org/10.1371/journal.pgen.1000748

Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 Locus

Jennifer L. Stonaker, Jana P. Lim, Karl F. Erhard Jr, Jay B. Hollick

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000706

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  2. RNA-Silencing Enzymes Pol IV and Pol V in Maize: More than one Flavor?

A Single Molecule Scaffold for the Maize Genome

Shiguo Zhou, Fusheng Wei, John Nguyen, Mike Bechner, Konstantinos Potamousis, Steve Goldstein, Louise Pape, Michael R. Mehan, Chris Churas, Shiran Pasternak, Dan K. Forrest, Roger Wise, Doreen Ware, Rod A. Wing, Michael S. Waterman, Miron Livny, David C. Schwartz

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000711

The Physical and Genetic Framework of the Maize B73 Genome

Fusheng Wei, Jianwei Zhang, Shiguo Zhou, Ruifeng He, Mary Schaeffer, Kristi Collura, David Kudrna, Ben P. Faga, Marina Wissotski, Wolfgang Golser, Susan M. Rock, Tina A. Graves, Robert S. Fulton, Ed Coe, Patrick S. Schnable, David C. Schwartz, Doreen Ware, Sandra W. Clifton, Richard K. Wilson, Rod A. Wing

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000715

A Genome-Wide Characterization of MicroRNA Genes in Maize

Lifang Zhang, Jer-Ming Chia, Sunita Kumari, Joshua C. Stein, Zhijie Liu, Apurva Narechania, Christopher A. Maher, Katherine Guill, Michael D. McMullen, Doreen Ware

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000716

A Dominant Mutation in mediator of paramutation2, One of Three Second-Largest Subunits of a Plant-Specific RNA Polymerase, Disrupts Multiple siRNA Silencing Processes

Lyudmila Sidorenko, Jane E. Dorweiler, A. Mark Cigan, Mario Arteaga-Vazquez, Meenal Vyas, Jerry Kermicle, Diane Jurcin, Jan Brzeski, Yu Cai, Vicki L. Chandler

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000725

Related Articles

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Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome

Fusheng Wei, Joshua C. Stein, Chengzhi Liang, Jianwei Zhang, Robert S. Fulton, Regina S. Baucom, Emanuele De Paoli, Shiguo Zhou, Lixing Yang, Yujun Han, Shiran Pasternak, Apurva Narechania, Lifang Zhang, Cheng-Ting Yeh, Kai Ying, Dawn H. Nagel, Kristi Collura, David Kudrna, Jennifer Currie, Jinke Lin, HyeRan Kim, Angelina Angelova, Gabriel Scara, Marina Wissotski, Wolfgang Golser, Laura Courtney, Scott Kruchowski, Tina A. Graves, Susan M. Rock, Stephanie Adams, Lucinda A. Fulton, Catrina Fronick, William Courtney, Melissa Kramer, Lori Spiegel, Lydia Nascimento, Ananth Kalyanaraman, Cristian Chaparro, Jean-Marc Deragon, Phillip San Miguel, Ning Jiang, Susan R. Wessler, Pamela J. Green, Yeisoo Yu, David C. Schwartz, Blake C. Meyers, Jeffrey L. Bennetzen, Robert A. Martienssen, W. Richard McCombie, Srinivas Aluru, Sandra W. Clifton, Patrick S. Schnable, Doreen Ware, Richard K. Wilson, Rod A. Wing

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000728

Fine-Scale Phylogenetic Discordance across the House Mouse Genome

Michael A. White, Cécile Ané, Colin N. Dewey, Bret R. Larget, Bret A. Payseur

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000729

Forty-Three Loci Associated with Plasma Lipoprotein Size, Concentration, and Cholesterol Content in Genome-Wide Analysis

Daniel I. Chasman, Guillaume Paré, Samia Mora, Jemma C. Hopewell, Gina Peloso, Robert Clarke, L. Adrienne Cupples, Anders Hamsten, Sekar Kathiresan, Anders Mälarstig, José M. Ordovas, Samuli Ripatti, Alex N. Parker, Joseph P. Miletich, Paul M. Ridker

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000730

Stage-Specific Expression Profiling of Drosophila Spermatogenesis Suggests that Meiotic Sex Chromosome Inactivation Drives Genomic Relocation of Testis-Expressed Genes

Maria D. Vibranovski, Hedibert F. Lopes, Timothy L. Karr, Manyuan Long

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000731

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Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

Regina S. Baucom, James C. Estill, Cristian Chaparro, Naadira Upshaw, Ansuya Jogi, Jean-Marc Deragon, Richard P. Westerman, Phillip J. SanMiguel, Jeffrey L. Bennetzen

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000732

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

Sanzhen Liu, Cheng-Ting Yeh, Tieming Ji, Kai Ying, Haiyan Wu, Ho Man Tang, Yan Fu, Dan Nettleton, Patrick S. Schnable

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000733

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Nathan M. Springer, Kai Ying, Yan Fu, Tieming Ji, Cheng-Ting Yeh, Yi Jia, Wei Wu, Todd Richmond, Jacob Kitzman, Heidi Rosenbaum, A. Leonardo Iniguez, W. Brad Barbazuk, Jeffrey A. Jeddeloh, Dan Nettleton, Patrick S. Schnable

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000734

Caenorhabditis elegans HIM-18/SLX-4 Interacts with SLX-1 and XPF-1 and Maintains Genomic Integrity in the Germline by Processing Recombination Intermediates

Takamune T. Saito, Jillian L. Youds, Simon J. Boulton, Monica P. Colaiácovo

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000735

Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

Yi Jia, Damon R. Lisch, Kazuhiro Ohtsu, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000737

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

Carol Soderlund, Anne Descour, Dave Kudrna, Matthew Bomhoff, Lomax Boyd, Jennifer Currie, Angelina Angelova, Kristi Collura, Marina Wissotski, Elizabeth Ashley, Darren Morrow, John Fernandes, Virginia Walbot, Yeisoo Yu

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000740

Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons

Thomas K. Wolfgruber, Anupma Sharma, Kevin L. Schneider, Patrice S. Albert, Dal-Hoe Koo, Jinghua Shi, Zhi Gao, Fangpu Han, Hyeran Lee, Ronghui Xu, Jamie Allison, James A. Birchler, Jiming Jiang, R. Kelly Dawe, Gernot G. Presting

PLOS Genetics: published November 20, 2009 | https://doi.org/10.1371/journal.pgen.1000743

The Pivotal Roles of TIA Proteins in 5′ Splice-Site Selection of Alu Exons and Across Evolution

Nurit Gal-Mark, Schraga Schwartz, Oren Ram, Eduardo Eyras, Gil Ast

PLOS Genetics: published November 13, 2009 | https://doi.org/10.1371/journal.pgen.1000717

A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells

Je-Hyuk Lee, In-Hyun Park, Yuan Gao, Jin Billy Li, Zhe Li, George Q. Daley, Kun Zhang, George M. Church

PLOS Genetics: published November 13, 2009 | https://doi.org/10.1371/journal.pgen.1000718

Gene Dosage, Expression, and Ontology Analysis Identifies Driver Genes in the Carcinogenesis and Chemoradioresistance of Cervical Cancer

Malin Lando, Marit Holden, Linn C. Bergersen, Debbie H. Svendsrud, Trond Stokke, Kolbein Sundfør, Ingrid K. Glad, Gunnar B. Kristensen, Heidi Lyng

PLOS Genetics: published November 13, 2009 | https://doi.org/10.1371/journal.pgen.1000719

Lgl2 Executes Its Function as a Tumor Suppressor by Regulating ErbB Signaling in the Zebrafish Epidermis

Sven Reischauer, Mitchell P. Levesque, Christiane Nüsslein-Volhard, Mahendra Sonawane

PLOS Genetics: published November 13, 2009 | https://doi.org/10.1371/journal.pgen.1000720

Evolutionary Convergence and Nitrogen Metabolism in Blattabacterium strain Bge, Primary Endosymbiont of the Cockroach Blattella germanica

Maria J. López-Sánchez, Alexander Neef, Juli Peretó, Rafael Patiño-Navarrete, Miguel Pignatelli, Amparo Latorre, Andrés Moya

PLOS Genetics: published November 13, 2009 | https://doi.org/10.1371/journal.pgen.1000721

Ctp1 and the MRN-Complex Are Required for Endonucleolytic Rec12 Removal with Release of a Single Class of Oligonucleotides in Fission Yeast

Maja Rothenberg, Jürg Kohli, Katja Ludin

PLOS Genetics: published November 13, 2009 | https://doi.org/10.1371/journal.pgen.1000722

The Schizosaccharomyces pombe JmjC-Protein, Msc1, Prevents H2A.Z Localization in Centromeric and Subtelomeric Chromatin Domains

Luke Buchanan, Mickaël Durand-Dubief, Assen Roguev, Cagri Sakalar, Brian Wilhelm, Annelie Strålfors, Anna Shevchenko, Rein Aasland, Andrej Shevchenko, Karl Ekwall, A. Francis Stewart

PLOS Genetics: published November 13, 2009 | https://doi.org/10.1371/journal.pgen.1000726

The Rts1 Regulatory Subunit of Protein Phosphatase 2A Is Required for Control of G1 Cyclin Transcription and Nutrient Modulation of Cell Size

Karen Artiles, Stephanie Anastasia, Derek McCusker, Douglas R. Kellogg

PLOS Genetics: published November 13, 2009 | https://doi.org/10.1371/journal.pgen.1000727

The Germ Cell Nuclear Proteins hnRNP G-T and RBMY Activate a Testis-Specific Exon

Yilei Liu, Cyril F. Bourgeois, Shaochen Pang, Marek Kudla, Natacha Dreumont, Liliane Kister, Yong-Hua Sun, James Stevenin, David J. Elliott

PLOS Genetics: published November 6, 2009 | https://doi.org/10.1371/journal.pgen.1000707

Mutations in the Caenorhabditis elegans U2AF Large Subunit UAF-1 Alter the Choice of a 3′ Splice Site In Vivo

Long Ma, H. Robert Horvitz

PLOS Genetics: published November 6, 2009 | https://doi.org/10.1371/journal.pgen.1000708

Functional Evolution of cis-Regulatory Modules at a Homeotic Gene in Drosophila

Margaret C. W. Ho, Holly Johnsen, Sara E. Goetz, Benjamin J. Schiller, Esther Bae, Diana A. Tran, Andrey S. Shur, John M. Allen, Christoph Rau, Welcome Bender, William W. Fisher, Susan E. Celniker, Robert A. Drewell

PLOS Genetics: published November 6, 2009 | https://doi.org/10.1371/journal.pgen.1000709

The Sir2-Sum1 Complex Represses Transcription Using Both Promoter-Specific and Long-Range Mechanisms to Regulate Cell Identity and Sexual Cycle in the Yeast Kluyveromyces lactis

Meleah A. Hickman, Laura N. Rusche

PLOS Genetics: published November 6, 2009 | https://doi.org/10.1371/journal.pgen.1000710

OAZ-t/OAZ3 Is Essential for Rigid Connection of Sperm Tails to Heads in Mouse

Keizo Tokuhiro, Ayako Isotani, Sadaki Yokota, Yoshihisa Yano, Shigeru Oshio, Mika Hirose, Morimasa Wada, Kyoko Fujita, Yukiko Ogawa, Masaru Okabe, Yoshitake Nishimune, Hiromitsu Tanaka

PLOS Genetics: published November 6, 2009 | https://doi.org/10.1371/journal.pgen.1000712

E Unibus Plurum: Genomic Analysis of an Experimentally Evolved Polymorphism in Escherichia coli

Margie A. Kinnersley, William E. Holben, Frank Rosenzweig

PLOS Genetics: published November 6, 2009 | https://doi.org/10.1371/journal.pgen.1000713

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

Paul J. McMurdie, Sebastian F. Behrens, Jochen A. Müller, Jonathan Göke, Kirsti M. Ritalahti, Ryan Wagner, Eugene Goltsman, Alla Lapidus, Susan Holmes, Frank E. Löffler, Alfred M. Spormann

PLOS Genetics: published November 6, 2009 | https://doi.org/10.1371/journal.pgen.1000714