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Table of Contents: November 2012

COVER

Cell division in Arabidopsis vascular tissue.

Image Credit: J. Peter Etchells and Simon R. Turner, The University of Manchester.
Issue Image

In plants, vascular tissue is responsible for providing water and nutrient transport and structural support, and it is derived from a group of dividing cells present in a structure called the procambium. In this issue, Etchells et al. used a reverse genetic approach to identify components that interact to control cell division in the procambium of Arabidopsis thaliana.

Perspectives

The Covariate's Dilemma

Joel Mefford, John S. Witte

Review

Research Articles

Lung eQTLs to Help Reveal the Molecular Underpinnings of Asthma

Ke Hao, Yohan Bossé, David C. Nickle, Peter D. Paré, Dirkje S. Postma, Michel Laviolette, Andrew Sandford, Tillie L. Hackett, Denise Daley, James C. Hogg, W. Mark Elliott, Christian Couture, Maxime Lamontagne, Corry-Anke Brandsma, Maarten van den Berge, Gerard Koppelman, Alise S. Reicin, Donald W. Nicholson, Vladislav Malkov, Jonathan M. Derry, Christine Suver, Jeffrey A. Tsou, Amit Kulkarni, Chunsheng Zhang, Rupert Vessey, Greg J. Opiteck, Sean P. Curtis, Wim Timens, Don D. Sin

A Genome-Scale RNA–Interference Screen Identifies RRAS Signaling as a Pathologic Feature of Huntington's Disease

John P. Miller, Bridget E. Yates, Ismael Al-Ramahi, Ari E. Berman, Mario Sanhueza, Eugene Kim, Maria de Haro, Francesco DeGiacomo, Cameron Torcassi, Jennifer Holcomb, Juliette Gafni, Sean D. Mooney, Juan Botas, Lisa M. Ellerby, Robert E. Hughes

Molecular, Physiological, and Motor Performance Defects in DMSXL Mice Carrying >1,000 CTG Repeats from the Human DM1 Locus

Aline Huguet, Fadia Medja, Annie Nicole, Alban Vignaud, Céline Guiraud-Dogan, Arnaud Ferry, Valérie Decostre, Jean-Yves Hogrel, Friedrich Metzger, Andreas Hoeflich, Martin Baraibar, Mário Gomes-Pereira, Jack Puymirat, Guillaume Bassez, Denis Furling, Arnold Munnich, Geneviève Gourdon

Transcription Elongation and Tissue-Specific Somatic CAG Instability

Agathi-Vasiliki Goula, Agnieszka Stys, Jackson P. K. Chan, Yvon Trottier, Richard Festenstein, Karine Merienne

Network Analysis of a Pkd1-Mouse Model of Autosomal Dominant Polycystic Kidney Disease Identifies HNF4α as a Disease Modifier

Luis F. Menezes, Fang Zhou, Andrew D. Patterson, Klaus B. Piontek, Kristopher W. Krausz, Frank J. Gonzalez, Gregory G. Germino

Loss of the DNA Methyltransferase MET1 Induces H3K9 Hypermethylation at PcG Target Genes and Redistribution of H3K27 Trimethylation to Transposons in Arabidopsis thaliana

Angelique Deleris, Hume Stroud, Yana Bernatavichute, Elizabeth Johnson, Gregor Klein, Daniel Schubert, Steven E. Jacobsen

Spastic Paraplegia Mutation N256S in the Neuronal Microtubule Motor KIF5A Disrupts Axonal Transport in a Drosophila HSP Model

Petra Füger, Vrinda Sreekumar, Rebecca Schüle, Jeannine V. Kern, Doychin T. Stanchev, Carola D. Schneider, Kathrin N. Karle, Katharina J. Daub, Vera K. Siegert, Matthias Flötenmeyer, Heinz Schwarz, Ludger Schöls, Tobias M. Rasse

CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function

Jacy L. Wagnon, Michael Briese, Wenzhi Sun, Connie L. Mahaffey, Tomaž Curk, Gregor Rot, Jernej Ule, Wayne N. Frankel

Tissue-Specific Regulation of Chromatin Insulator Function

Leah H. Matzat, Ryan K. Dale, Nellie Moshkovich, Elissa P. Lei

Initiation of Genome Instability and Preneoplastic Processes through Loss of Fhit Expression

Joshua C. Saldivar, Satoshi Miuma, Jessica Bene, Seyed Ali Hosseini, Hidetaka Shibata, Jin Sun, Linda J. Wheeler, Christopher K. Mathews, Kay Huebner

dJun and Vri/dNFIL3 Are Major Regulators of Cardiac Aging in Drosophila

Véronique Monnier, Magali Iché-Torres, Michael Rera, Vincent Contremoulins, Céline Guichard, Nathalie Lalevée, Hervé Tricoire, Laurent Perrin

Discovering Thiamine Transporters as Targets of Chloroquine Using a Novel Functional Genomics Strategy

Zhiwei Huang, Sankaranarayanan Srinivasan, Jianhuai Zhang, Kaifu Chen, Yongxiang Li, Wei Li, Florante A. Quiocho, Xuewen Pan

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

Pierre J. G. M. de Wit, Ate van der Burgt, Bilal Ökmen, Ioannis Stergiopoulos, Kamel A. Abd-Elsalam, Andrea L. Aerts, Ali H. Bahkali, Henriek G. Beenen, Pranav Chettri, Murray P. Cox, Erwin Datema, Ronald P. de Vries, Braham Dhillon, Austen R. Ganley, Scott A. Griffiths, Yanan Guo, Richard C. Hamelin, Bernard Henrissat, M. Shahjahan Kabir, Mansoor Karimi Jashni, Gert Kema, Sylvia Klaubauf, Alla Lapidus, Anthony Levasseur, Erika Lindquist, Rahim Mehrabi, Robin A. Ohm, Timothy J. Owen, Asaf Salamov, Arne Schwelm, Elio Schijlen, Hui Sun, Harrold A. van den Burg, Roeland C. H. J. van Ham, Shuguang Zhang, Stephen B. Goodwin, Igor V. Grigoriev, Jérôme Collemare, Rosie E. Bradshaw

MicroRNA–Mediated Repression of the Seed Maturation Program during Vegetative Development in Arabidopsis

Xurong Tang, Shaomin Bian, Mingjuan Tang, Qing Lu, Shengben Li, Xigang Liu, Gang Tian, Vi Nguyen, Edward W. T. Tsang, Aiming Wang, Steven J. Rothstein, Xuemei Chen, Yuhai Cui

Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape

Mirte Bosse, Hendrik-Jan Megens, Ole Madsen, Yogesh Paudel, Laurent A. F. Frantz, Lawrence B. Schook, Richard P. M. A. Crooijmans, Martien A. M. Groenen

The Yeast SR-Like Protein Npl3 Links Chromatin Modification to mRNA Processing

Erica A. Moehle, Colm J. Ryan, Nevan J. Krogan, Tracy L. Kress, Christine Guthrie

The Principal Genetic Determinants for Nasopharyngeal Carcinoma in China Involve the HLA Class I Antigen Recognition Groove

Minzhong Tang, James A. Lautenberger, Xiaojiang Gao, Efe Sezgin, Sher L. Hendrickson, Jennifer L. Troyer, Victor A. David, Li Guan, Carl E. Mcintosh, Xiuchan Guo, Yuming Zheng, Jian Liao, Hong Deng, Michael Malasky, Bailey Kessing, Cheryl A. Winkler, Mary Carrington, Guy dé The, Yi Zeng, Stephen J. O'Brien

Zcchc11 Uridylates Mature miRNAs to Enhance Neonatal IGF-1 Expression, Growth, and Survival

Matthew R. Jones, Matthew T. Blahna, Elyse Kozlowski, Kori Y. Matsuura, Joseph D. Ferrari, Samantha A. Morris, John T. Powers, George Q. Daley, Lee J. Quinton, Joseph P. Mizgerd

A Novel Human-Infection-Derived Bacterium Provides Insights into the Evolutionary Origins of Mutualistic Insect–Bacterial Symbioses

Adam L. Clayton, Kelly F. Oakeson, Maria Gutin, Arthur Pontes, Diane M. Dunn, Andrew C. von Niederhausern, Robert B. Weiss, Mark Fisher, Colin Dale

Disruption of Mouse Cenpj, a Regulator of Centriole Biogenesis, Phenocopies Seckel Syndrome

Rebecca E. McIntyre, Pavithra Lakshminarasimhan Chavali, Ozama Ismail, Damian M. Carragher, Gabriela Sanchez-Andrade, Josep V. Forment, Beiyuan Fu, Martin Del Castillo Velasco-Herrera, Andrew Edwards, Louise van der Weyden, Fengtang Yang, Ramiro Ramirez-Solis, Jeanne Estabel, Ferdia A. Gallagher, Darren W. Logan, Mark J. Arends, Stephen H. Tsang, Vinit B. Mahajan, Cheryl L. Scudamore, Jacqueline K. White, Stephen P. Jackson, Fanni Gergely, David J. Adams , Sanger Mouse Genetics Project

Cooperativity of Rb, Brca1, and p53 in Malignant Breast Cancer Evolution

Prashant Kumar, Malini Mukherjee, Jacob P. S. Johnson, Milan Patel, Bing Huey, Donna G. Albertson, Karl Simin

Genomic Study of RNA Polymerase II and III SNAPc-Bound Promoters Reveals a Gene Transcribed by Both Enzymes and a Broad Use of Common Activators

Nicole James Faresse, Donatella Canella, Viviane Praz, Joëlle Michaud, David Romascano, Nouria Hernandez

Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers

Chiara Boschetti, Adrian Carr, Alastair Crisp, Isobel Eyres, Yuan Wang-Koh, Esther Lubzens, Timothy G. Barraclough, Gos Micklem, Alan Tunnacliffe

Controls of Nucleosome Positioning in the Human Genome

Daniel J. Gaffney, Graham McVicker, Athma A. Pai, Yvonne N. Fondufe-Mittendorf, Noah Lewellen, Katelyn Michelini, Jonathan Widom, Yoav Gilad, Jonathan K. Pritchard

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Andreas Massouras, Sebastian M. Waszak, Monica Albarca-Aguilera, Korneel Hens, Wiebke Holcombe, Julien F. Ayroles, Emmanouil T. Dermitzakis, Eric A. Stone, Jeffrey D. Jensen, Trudy F. C. Mackay, Bart Deplancke

Genome-Wide Association Studies Reveal a Simple Genetic Basis of Resistance to Naturally Coevolving Viruses in Drosophila melanogaster

Michael M. Magwire, Daniel K. Fabian, Hannah Schweyen, Chuan Cao, Ben Longdon, Florian Bayer, Francis M. Jiggins

RHOA Is a Modulator of the Cholesterol-Lowering Effects of Statin

Marisa W. Medina, Elizabeth Theusch, Devesh Naidoo, Frederick Bauzon, Kristen Stevens, Lara M. Mangravite, Yu-Lin Kuang, Ronald M. Krauss

Lamin B1 Polymorphism Influences Morphology of the Nuclear Envelope, Cell Cycle Progression, and Risk of Neural Tube Defects in Mice

Sandra C. P. De Castro, Ashraf Malhas, Kit-Yi Leung, Peter Gustavsson, David J. Vaux, Andrew J. Copp, Nicholas D. E. Greene

HP1a Recruitment to Promoters Is Independent of H3K9 Methylation in Drosophila melanogaster

Margarida L. A. Figueiredo, Philge Philip, Per Stenberg, Jan Larsson

Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779

Astrid Vieler, Guangxi Wu, Chia-Hong Tsai, Blair Bullard, Adam J. Cornish, Christopher Harvey, Ida-Barbara Reca, Chelsea Thornburg, Rujira Achawanantakun, Christopher J. Buehl, Michael S. Campbell, David Cavalier, Kevin L. Childs, Teresa J. Clark, Rahul Deshpande, Erika Erickson, Ann Armenia Ferguson, Witawas Handee, Que Kong, Xiaobo Li, Bensheng Liu, Steven Lundback, Cheng Peng, Rebecca L. Roston, Sanjaya, Jeffrey P. Simpson, Allan TerBush, Jaruswan Warakanont, Simone Zäuner, Eva M. Farre, Eric L. Hegg, Ning Jiang, Min-Hao Kuo, Yan Lu, Krishna K. Niyogi, John Ohlrogge, Katherine W. Osteryoung, Yair Shachar-Hill, Barbara B. Sears, Yanni Sun, Hideki Takahashi, Mark Yandell, Shin-Han Shiu, Christoph Benning

Evolution of Minimal Specificity and Promiscuity in Steroid Hormone Receptors

Geeta N. Eick, Jennifer K. Colucci, Michael J. Harms, Eric A. Ortlund, Joseph W. Thornton

The Contributions of Wobbling and Superwobbling to the Reading of the Genetic Code

Sibah Alkatib, Lars B. Scharff, Marcelo Rogalski, Tobias T. Fleischmann, Annemarie Matthes, Stefanie Seeger, Mark A. Schöttler, Stephanie Ruf, Ralph Bock

Polyadenylation-Dependent Control of Long Noncoding RNA Expression by the Poly(A)-Binding Protein Nuclear 1

Yves B. Beaulieu, Claudia L. Kleinman, Anne-Marie Landry-Voyer, Jacek Majewski, François Bachand

Comparison of Mitochondrial Mutation Spectra in Ageing Human Colonic Epithelium and Disease: Absence of Evidence for Purifying Selection in Somatic Mitochondrial DNA Point Mutations

Laura C. Greaves, Joanna L. Elson, Marco Nooteboom, John P. Grady, Geoffrey A. Taylor, Robert W. Taylor, John C. Mathers, Thomas B. L. Kirkwood, Doug M. Turnbull

Identification of the First ATRIP–Deficient Patient and Novel Mutations in ATR Define a Clinical Spectrum for ATR–ATRIP Seckel Syndrome

Tomoo Ogi, Sarah Walker, Tom Stiff, Emma Hobson, Siripan Limsirichaikul, Gillian Carpenter, Katrina Prescott, Mohnish Suri, Philip J. Byrd, Michiko Matsuse, Norisato Mitsutake, Yuka Nakazawa, Pradeep Vasudevan, Margaret Barrow, Grant S. Stewart, A. Malcolm R. Taylor, Mark O'Driscoll, Penny A. Jeggo

Evolutionarily Ancient Association of the FoxJ1 Transcription Factor with the Motile Ciliogenic Program

Shubha Vij, Jochen C. Rink, Hao Kee Ho, Deepak Babu, Michael Eitel, Vijayashankaranarayanan Narasimhan, Varnesh Tiku, Jody Westbrook, Bernd Schierwater, Sudipto Roy

Loss of Prohibitin Membrane Scaffolds Impairs Mitochondrial Architecture and Leads to Tau Hyperphosphorylation and Neurodegeneration

Carsten Merkwirth, Paola Martinelli, Anne Korwitz, Michela Morbin, Hella S. Brönneke, Sabine D. Jordan, Elena I. Rugarli, Thomas Langer

Microhomology Directs Diverse DNA Break Repair Pathways and Chromosomal Translocations

Diana D. Villarreal, Kihoon Lee, Angela Deem, Eun Yong Shim, Anna Malkova, Sang Eun Lee

Mechanisms Employed by Escherichia coli to Prevent Ribonucleotide Incorporation into Genomic DNA by Pol V

John P. McDonald, Alexandra Vaisman, Wojciech Kuban, Myron F. Goodman, Roger Woodgate

Informed Conditioning on Clinical Covariates Increases Power in Case-Control Association Studies

Noah Zaitlen, Sara Lindström, Bogdan Pasaniuc, Marilyn Cornelis, Giulio Genovese, Samuela Pollack, Anne Barton, Heike Bickeböller, Donald W. Bowden, Steve Eyre, Barry I. Freedman, David J. Friedman, John K. Field, Leif Groop, Aage Haugen, Joachim Heinrich, Brian E. Henderson, Pamela J. Hicks, Lynne J. Hocking, Laurence N. Kolonel, Maria Teresa Landi, Carl D. Langefeld, Loic Le Marchand, Michael Meister, Ann W. Morgan, Olaide Y. Raji, Angela Risch, Albert Rosenberger, David Scherf, Sophia Steer, Martin Walshaw, Kevin M. Waters, Anthony G. Wilson, Paul Wordsworth, Shanbeh Zienolddiny, Eric Tchetgen Tchetgen, Christopher Haiman, David J. Hunter, Robert M. Plenge, Jane Worthington, David C. Christiani, Debra A. Schaumberg, Daniel I. Chasman, David Altshuler, Benjamin Voight, Peter Kraft, Nick Patterson, Alkes L. Price

The DNA Replication Factor RFC1 Is Required for Interference-Sensitive Meiotic Crossovers in Arabidopsis thaliana

Yingxiang Wang, Zhihao Cheng, Jiyue Huang, Qian Shi, Yue Hong, Gregory P. Copenhaver, Zhizhong Gong, Hong Ma

CNOT3 Is a Modifier of PRPF31 Mutations in Retinitis Pigmentosa with Incomplete Penetrance

Giulia Venturini, Anna M. Rose, Amna Z. Shah, Shomi S. Bhattacharya, Carlo Rivolta

A Combination of H2A.Z and H4 Acetylation Recruits Brd2 to Chromatin during Transcriptional Activation

Ryan Draker, Marlee K. Ng, Elizabeth Sarcinella, Vladimir Ignatchenko, Thomas Kislinger, Peter Cheung

Transcription Factor Oct1 Is a Somatic and Cancer Stem Cell Determinant

Jessica Maddox, Arvind Shakya, Samuel South, Dawne Shelton, Jared N. Andersen, Stephanie Chidester, Jinsuk Kang, Keith M. Gligorich, David A. Jones, Gerald J. Spangrude, Bryan E. Welm, Dean Tantin

CtIP Is Required to Initiate Replication-Dependent Interstrand Crosslink Repair

Michelle L. Duquette, Qingyuan Zhu, Ewan R. Taylor, Angela J. Tsay, Linda Z. Shi, Michael W. Berns, Clare H. McGowan

Population Genomic Scan for Candidate Signatures of Balancing Selection to Guide Antigen Characterization in Malaria Parasites

Alfred Amambua-Ngwa, Kevin K. A. Tetteh, Magnus Manske, Natalia Gomez-Escobar, Lindsay B. Stewart, M. Elizabeth Deerhake, Ian H. Cheeseman, Christopher I. Newbold, Anthony A. Holder, Ellen Knuepfer, Omar Janha, Muminatou Jallow, Susana Campino, Bronwyn MacInnis, Dominic P. Kwiatkowski, David J. Conway

Disruption of Chtf18 Causes Defective Meiotic Recombination in Male Mice

Karen M. Berkowitz, Aislinn R. Sowash, Lydia R. Koenig, Dawnette Urcuyo, Fahmida Khan, Fang Yang, P. Jeremy Wang, Thomas A. Jongens, Klaus H. Kaestner

Antagonistic Gene Activities Determine the Formation of Pattern Elements along the Mediolateral Axis of the Arabidopsis Fruit

Santiago González-Reig, Juan José Ripoll, Antonio Vera, Martin F. Yanofsky, Antonio Martínez-Laborda

Stimulation of Gross Chromosomal Rearrangements by the Human CEB1 and CEB25 Minisatellites in Saccharomyces cerevisiae Depends on G-Quadruplexes or Cdc13

Aurèle Piazza, Alexandre Serero, Jean-Baptiste Boulé, Patricia Legoix-Né, Judith Lopes, Alain Nicolas

A Dominantly Acting Murine Allele of Mcm4 Causes Chromosomal Abnormalities and Promotes Tumorigenesis

Bruce N. Bagley, Thomas M. Keane, Vilena I. Maklakova, Jonathon G. Marshall, Rachael A. Lester, Michelle M. Cancel, Alex R. Paulsen, Laura E. Bendzick, Raha A. Been, Scott C. Kogan, Robert T. Cormier, Christina Kendziorski, David J. Adams, Lara S. Collier

A Bacteriophage-Encoded J-Domain Protein Interacts with the DnaK/Hsp70 Chaperone and Stabilizes the Heat-Shock Factor σ32 of Escherichia coli

Elsa Perrody, Anne-Marie Cirinesi, Carine Desplats, France Keppel, Françoise Schwager, Samuel Tranier, Costa Georgopoulos, Pierre Genevaux

Interallelic and Intergenic Incompatibilities of the Prdm9 (Hst1) Gene in Mouse Hybrid Sterility

Petr Flachs, Ondřej Mihola, Petr Šimeček, Soňa Gregorová, John C. Schimenti, Yasuhisa Matsui, Frédéric Baudat, Bernard de Massy, Jaroslav Piálek, Jiří Forejt, Zdenek Trachtulec