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Table of Contents

August 2009

Cover

A bundle of green fluorescent protein-expressing pollen tubes emerge from an Arabidopsis thaliana pistil explant.
Issue Image

In flowering plants, pollen tubes germinate on the stigma surface and extend through the pistil to locate and deliver sperm to female gametes. An article in this issue of PLoS Genetics (see Qin et al, 10.1371/journal.pgen.1000621) uses bundles of pistil-grown pollen tubes, similar to those shown here, to define genome-wide changes in Arabidopsis pollen tube gene expression that occur in response to growth through pistil tissue. Dramatic changes in gene expression occur in pistil-grown tubes and point to genes that are required for the ability of pollen tubes to grow and reach their cellular targets.

Image Credit: Ravishankar Palanivelu (University of Arizona).

Perspectives

SCA8 CAG/CTG Expansions, a Tale of Two TOXICities: A Unique or Common Case?

Karine Merienne, Yvon Trottier

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000593

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Forests of the Night: Refugia of Genetic Diversity in Wild Tigers

Oliver A. Ryder

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000603

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Review

Alternative Mechanisms for Tn5 Transposition

Asad Ahmed

PLOS Genetics: published August 28, 2009 | https://doi.org/10.1371/journal.pgen.1000619

Research Articles

Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context

Brock C. Christensen, E. Andres Houseman, Carmen J. Marsit, Shichun Zheng, Margaret R. Wrensch, Joseph L. Wiemels, Heather H. Nelson, Margaret R. Karagas, James F. Padbury, Raphael Bueno, David J. Sugarbaker, Ru-Fang Yeh, John K. Wiencke, Karl T. Kelsey

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000602

Why the Indian Subcontinent Holds the Key to Global Tiger Recovery

Samrat Mondol, K. Ullas Karanth, Uma Ramakrishnan

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000585

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Nonredundant Requirement for Multiple Histone Modifications for the Early Anaphase Release of the Mitotic Exit Regulator Cdc14 from Nucleolar Chromatin

William W. Hwang, Hiten D. Madhani

PLOS Genetics: published August 7, 2009 | https://doi.org/10.1371/journal.pgen.1000588

A High Incidence of Meiotic Silencing of Unsynapsed Chromatin Is Not Associated with Substantial Pachytene Loss in Heterozygous Male Mice Carrying Multiple Simple Robertsonian Translocations

Marcia Manterola, Jesús Page, Chiara Vasco, Soledad Berríos, María Teresa Parra, Alberto Viera, Julio S. Rufas, Maurizio Zuccotti, Silvia Garagna, Raúl Fernández-Donoso

PLOS Genetics: published August 28, 2009 | https://doi.org/10.1371/journal.pgen.1000625

The Drosophila SH2B Family Adaptor Lnk Acts in Parallel to Chico in the Insulin Signaling Pathway

Christian Werz, Katja Köhler, Ernst Hafen, Hugo Stocker

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000596

Nuclear Calcium Signaling Controls Expression of a Large Gene Pool: Identification of a Gene Program for Acquired Neuroprotection Induced by Synaptic Activity

Sheng-Jia Zhang, Ming Zou, Li Lu, David Lau, Désirée A. W. Ditzel, Celine Delucinge-Vivier, Yoshinori Aso, Patrick Descombes, Hilmar Bading

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000604

A Link among DNA Replication, Recombination, and Gene Expression Revealed by Genetic and Genomic Analysis of TEBICHI Gene of Arabidopsis thaliana

Soichi Inagaki, Kenzo Nakamura, Atsushi Morikami

PLOS Genetics: published August 21, 2009 | https://doi.org/10.1371/journal.pgen.1000613

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

Jasmina Ponjavic, Peter L. Oliver, Gerton Lunter, Chris P. Ponting

PLOS Genetics: published August 21, 2009 | https://doi.org/10.1371/journal.pgen.1000617

Statistical Estimation of Correlated Genome Associations to a Quantitative Trait Network

Seyoung Kim, Eric P. Xing

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000587

Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence

Dara G. Torgerson, Adam R. Boyko, Ryan D. Hernandez, Amit Indap, Xiaolan Hu, Thomas J. White, John J. Sninsky, Michele Cargill, Mark D. Adams, Carlos D. Bustamante, Andrew G. Clark

PLOS Genetics: published August 7, 2009 | https://doi.org/10.1371/journal.pgen.1000592

Regulation of Heterochromatin Assembly on Unpaired Chromosomes during Caenorhabditis elegans Meiosis by Components of a Small RNA-Mediated Pathway

Xingyu She, Xia Xu, Alexander Fedotov, William G. Kelly, Eleanor M. Maine

PLOS Genetics: published August 28, 2009 | https://doi.org/10.1371/journal.pgen.1000624

Osteo-Chondroprogenitor–Specific Deletion of the Selenocysteine tRNA Gene, Trsp, Leads to Chondronecrosis and Abnormal Skeletal Development: A Putative Model for Kashin-Beck Disease

Charlene M. Downey, Chelsea R. Horton, Bradley A. Carlson, Trish E. Parsons, Dolph L. Hatfield, Benedikt Hallgrímsson, Frank R. Jirik

PLOS Genetics: published August 21, 2009 | https://doi.org/10.1371/journal.pgen.1000616

A Claudin-9–Based Ion Permeability Barrier Is Essential for Hearing

Yoko Nakano, Sung H. Kim, Hyoung-Mi Kim, Joel D. Sanneman, Yuzhou Zhang, Richard J. H. Smith, Daniel C. Marcus, Philine Wangemann, Randy A. Nessler, Botond Bánfi

PLOS Genetics: published August 21, 2009 | https://doi.org/10.1371/journal.pgen.1000610

The Drosophila foraging Gene Mediates Adult Plasticity and Gene–Environment Interactions in Behaviour, Metabolites, and Gene Expression in Response to Food Deprivation

Clement F. Kent, Tim Daskalchuk, Lisa Cook, Marla B. Sokolowski, Ralph J. Greenspan

PLOS Genetics: published August 21, 2009 | https://doi.org/10.1371/journal.pgen.1000609

Regulon-Specific Control of Transcription Elongation across the Yeast Genome

Vicent Pelechano, Silvia Jimeno-González, Alfonso Rodríguez-Gil, José García-Martínez, José E. Pérez-Ortín, Sebastián Chávez

PLOS Genetics: published August 21, 2009 | https://doi.org/10.1371/journal.pgen.1000614

Notch and Prospero Repress Proliferation following Cyclin E Overexpression in the Drosophila Bristle Lineage

Françoise Simon, Pierre Fichelson, Michel Gho, Agnès Audibert

PLOS Genetics: published August 7, 2009 | https://doi.org/10.1371/journal.pgen.1000594

The Population and Evolutionary Dynamics of Homologous Gene Recombination in Bacteria

Bruce R. Levin, Omar E. Cornejo

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000601

A Computational Screen for Regulators of Oxidative Phosphorylation Implicates SLIRP in Mitochondrial RNA Homeostasis

Joshua M. Baughman, Roland Nilsson, Vishal M. Gohil, Daniel H. Arlow, Zareen Gauhar, Vamsi K. Mootha

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000590

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CLRN1 Is Nonessential in the Mouse Retina but Is Required for Cochlear Hair Cell Development

Scott F. Geller, Karen I. Guerin, Meike Visel, Aaron Pham, Edwin S. Lee, Amiel A. Dror, Karen B. Avraham, Toshinori Hayashi, Catherine A. Ray, Thomas A. Reh, Olivia Bermingham-McDonogh, William J. Triffo, Shaowen Bao, Juha Isosomppi, Hanna Västinsalo, Eeva-Marja Sankila, John G. Flannery

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000607

Tissue Effect on Genetic Control of Transcript Isoform Variation

Tony Kwan, Elin Grundberg, Vonda Koka, Bing Ge, Kevin C. L. Lam, Christel Dias, Andreas Kindmark, Hans Mallmin, Östen Ljunggren, Fernando Rivadeneira, Karol Estrada, Joyce B. van Meurs, Andre Uitterlinden, Magnus Karlsson, Claes Ohlsson, Dan Mellström, Olle Nilsson, Tomi Pastinen, Jacek Majewski

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000608

P-Type ATPase TAT-2 Negatively Regulates Monomethyl Branched-Chain Fatty Acid Mediated Function in Post-Embryonic Growth and Development in C. elegans

Emylie Seamen, Jennifer M. Blanchette, Min Han

PLOS Genetics: published August 7, 2009 | https://doi.org/10.1371/journal.pgen.1000589

The CUGBP2 Splicing Factor Regulates an Ensemble of Branchpoints from Perimeter Binding Sites with Implications for Autoregulation

Jill A. Dembowski, Paula J. Grabowski

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000595

Genome-Wide Association Study Implicates Chromosome 9q21.31 as a Susceptibility Locus for Asthma in Mexican Children

Dana B. Hancock, Isabelle Romieu, Min Shi, Juan-Jose Sienra-Monge, Hao Wu, Grace Y. Chiu, Huiling Li, Blanca Estela del Rio-Navarro, Saffron A. G. Willis-Owens, Scott T. Weiss, Benjamin A. Raby, Hong Gao, Celeste Eng, Rocio Chapela, Esteban G. Burchard, Hua Tang, Patrick F. Sullivan, Stephanie J. London

PLOS Genetics: published August 28, 2009 | https://doi.org/10.1371/journal.pgen.1000623

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A Mouse Model for the Metabolic Effects of the Human Fat Mass and Obesity Associated FTO Gene

Chris Church, Sheena Lee, Eleanor A. L. Bagg, James S. McTaggart, Robert Deacon, Thomas Gerken, Angela Lee, Lee Moir, Jasmin Mecinović, Mohamed M. Quwailid, Christopher J. Schofield, Frances M. Ashcroft, Roger D. Cox

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000599

RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

Randy S. Daughters, Daniel L. Tuttle, Wangcai Gao, Yoshio Ikeda, Melinda L. Moseley, Timothy J. Ebner, Maurice S. Swanson, Laura P. W. Ranum

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000600

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Production and Processing of siRNA Precursor Transcripts from the Highly Repetitive Maize Genome

Christopher J. Hale, Karl F. Erhard Jr., Damon Lisch, Jay B. Hollick

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000598

Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus

Li Jia, Gilad Landan, Mark Pomerantz, Rami Jaschek, Paula Herman, David Reich, Chunli Yan, Omar Khalid, Phil Kantoff, William Oh, J. Robert Manak, Benjamin P. Berman, Brian E. Henderson, Baruch Frenkel, Christopher A. Haiman, Matthew Freedman, Amos Tanay, Gerhard A. Coetzee

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000597

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

Jeffrey J. Coleman, Steve D. Rounsley, Marianela Rodriguez-Carres, Alan Kuo, Catherine C. Wasmann, Jane Grimwood, Jeremy Schmutz, Masatoki Taga, Gerard J. White, Shiguo Zhou, David C. Schwartz, Michael Freitag, Li-jun Ma, Etienne G. J. Danchin, Bernard Henrissat, Pedro M. Coutinho, David R. Nelson, Dave Straney, Carolyn A. Napoli, Bridget M. Barker, Michael Gribskov, Martijn Rep, Scott Kroken, István Molnár, Christopher Rensing, John C. Kennell, Jorge Zamora, Mark L. Farman, Eric U. Selker, Asaf Salamov, Harris Shapiro, Jasmyn Pangilinan, Erika Lindquist, Casey Lamers, Igor V. Grigoriev, David M. Geiser, Sarah F. Covert, Esteban Temporini, Hans D. VanEtten

PLOS Genetics: published August 28, 2009 | https://doi.org/10.1371/journal.pgen.1000618

Highly Dynamic and Sex-Specific Expression of microRNAs During Early ES Cell Differentiation

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CHD3 Proteins and Polycomb Group Proteins Antagonistically Determine Cell Identity in Arabidopsis

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PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000605

The Fission Yeast Homeodomain Protein Yox1p Binds to MBF and Confines MBF-Dependent Cell-Cycle Transcription to G1-S via Negative Feedback

Sofia Aligianni, Daniel H. Lackner, Steffi Klier, Gabriella Rustici, Brian T. Wilhelm, Samuel Marguerat, Sandra Codlin, Alvis Brazma, Robertus A. M. de Bruin, Jürg Bähler

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Spermatogenesis-Specific Features of the Meiotic Program in Caenorhabditis elegans

Diane C. Shakes, Jui-ching Wu, Penny L. Sadler, Kristen LaPrade, Landon L. Moore, Alana Noritake, Diana S. Chu

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Multiple Loci within the Major Histocompatibility Complex Confer Risk of Psoriasis

Bing-Jian Feng, Liang-Dan Sun, Razieh Soltani-Arabshahi, Anne M. Bowcock, Rajan P. Nair, Philip Stuart, James T. Elder, Steven J. Schrodi, Ann B. Begovich, Gonçalo R. Abecasis, Xue-Jun Zhang, Kristina P. Callis-Duffin, Gerald G. Krueger, David E. Goldgar

PLOS Genetics: published August 14, 2009 | https://doi.org/10.1371/journal.pgen.1000606

Identification of the UBP1 Locus as a Critical Blood Pressure Determinant Using a Combination of Mouse and Human Genetics

Hana Koutnikova, Markku Laakso, Lu Lu, Roy Combe, Jussi Paananen, Teemu Kuulasmaa, Johanna Kuusisto, Hans-Ulrich Häring, Torben Hansen, Oluf Pedersen, Ulf Smith, Markolf Hanefeld, Robert W. Williams, Johan Auwerx

PLOS Genetics: published August 7, 2009 | https://doi.org/10.1371/journal.pgen.1000591

Phosphofructo-1-Kinase Deficiency Leads to a Severe Cardiac and Hematological Disorder in Addition to Skeletal Muscle Glycogenosis

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PLOS Genetics: published August 21, 2009 | https://doi.org/10.1371/journal.pgen.1000615

Penetration of the Stigma and Style Elicits a Novel Transcriptome in Pollen Tubes, Pointing to Genes Critical for Growth in a Pistil

Yuan Qin, Alexander R. Leydon, Ann Manziello, Ritu Pandey, David Mount, Stojan Denic, Bane Vasic, Mark A. Johnson, Ravishankar Palanivelu

PLOS Genetics: published August 28, 2009 | https://doi.org/10.1371/journal.pgen.1000621

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Fission Yeast Tel1ATM and Rad3ATR Promote Telomere Protection and Telomerase Recruitment

Bettina A. Moser, Lakxmi Subramanian, Lyne Khair, Ya-Ting Chang, Toru M. Nakamura

PLOS Genetics: published August 28, 2009 | https://doi.org/10.1371/journal.pgen.1000622