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Table of Contents: July 2015

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Meiosis underpins sexual reproduction in higher eukaryotes. During this division, crossovers (COs) generate novel genotypes and guarantee the correct segregation of homologous chromosomes at anaphase I. The formation of COs is fine-tuned by several mechanisms. One of them, reported in some model organisms, is CO homeostasis, which ensures a stable number of COs despite variability in the number of initiating events. The analysis of Atfas1-4, which has a significant increase in double-strand breaks and in the frequency of gene conversion events, without a corresponding increase in COs, suggests the possible existence of a homeostatic control of COs in Arabidopsis. Varas et al.

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Perspectives

LINE-1 Retroelements Get ZAPped!

Richard N. McLaughlin Jr., Harmit S. Malik

Research Articles

MoSET1 (Histone H3K4 Methyltransferase in Magnaporthe oryzae) Regulates Global Gene Expression during Infection-Related Morphogenesis

Kieu Thi Minh Pham, Yoshihiro Inoue, Ba Van Vu, Hanh Hieu Nguyen, Toru Nakayashiki, Ken-ichi Ikeda, Hitoshi Nakayashiki

Corp Regulates P53 in Drosophila melanogaster via a Negative Feedback Loop

Riddhita Chakraborty, Ying Li, Lei Zhou, Kent G. Golic

A Genetic Incompatibility Accelerates Adaptation in Yeast

Duyen T. Bui, Elliot Dine, James B. Anderson, Charles F. Aquadro, Eric E. Alani

The Shelterin TIN2 Subunit Mediates Recruitment of Telomerase to Telomeres

Amanda K. Frank, Duy C. Tran, Roy W. Qu, Bradley A. Stohr, David J. Segal, Lifeng Xu

JAK/STAT and Hox Dynamic Interactions in an Organogenetic Gene Cascade

Pedro B. Pinto, Jose Manuel Espinosa-Vázquez, María Luísa Rivas, James Castelli-Gair Hombría

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

David J. Roach, Joshua N. Burton, Choli Lee, Bethany Stackhouse, Susan M. Butler-Wu, Brad T. Cookson, Jay Shendure, Stephen J. Salipante

BMP Inhibition in Seminomas Initiates Acquisition of Pluripotency via NODAL Signaling Resulting in Reprogramming to an Embryonal Carcinoma

Daniel Nettersheim, Sina Jostes, Rakesh Sharma, Simon Schneider, Andrea Hofmann, Humberto J. Ferreira, Per Hoffmann, Glen Kristiansen, Manel B. Esteller, Hubert Schorle

EIN3 and ORE1 Accelerate Degreening during Ethylene-Mediated Leaf Senescence by Directly Activating Chlorophyll Catabolic Genes in Arabidopsis

Kai Qiu, Zhongpeng Li, Zhen Yang, Junyi Chen, Shouxin Wu, Xiaoyu Zhu, Shan Gao, Jiong Gao, Guodong Ren, Benke Kuai, Xin Zhou

Checkpoint Activation of an Unconventional DNA Replication Program in Tetrahymena

Pamela Y. Sandoval, Po-Hsuen Lee, Xiangzhou Meng, Geoffrey M. Kapler

CSB-PGBD3 Mutations Cause Premature Ovarian Failure

Yingying Qin, Ting Guo, Guangyu Li, Tie-Shan Tang, Shidou Zhao, Xue Jiao, Juanjuan Gong, Fei Gao, Caixia Guo, Joe Leigh Simpson, Zi-Jiang Chen

Molecular Framework of a Regulatory Circuit Initiating Two-Dimensional Spatial Patterning of Stomatal Lineage

Robin J. Horst, Hironori Fujita, Jin Suk Lee, Amanda L. Rychel, Jacqueline M. Garrick, Masayoshi Kawaguchi, Kylee M. Peterson, Keiko U. Torii

Hairless Streaks in Cattle Implicate TSR2 in Early Hair Follicle Formation

Leonardo Murgiano, Vera Shirokova, Monika Maria Welle, Vidhya Jagannathan, Philippe Plattet, Anna Oevermann, Aldona Pienkowska-Schelling, Daniele Gallo, Arcangelo Gentile, Marja Mikkola, Cord Drögemüller

Large-Scale Phenomics Identifies Primary and Fine-Tuning Roles for CRKs in Responses Related to Oxidative Stress

Gildas Bourdais, Paweł Burdiak, Adrien Gauthier, Lisette Nitsch, Jarkko Salojärvi, Channabasavangowda Rayapuram, Niina Idänheimo, Kerri Hunter, Sachie Kimura, Ebe Merilo, Aleksia Vaattovaara, Krystyna Oracz, David Kaufholdt, Andres Pallon, Damar Tri Anggoro, Dawid Glów, Jennifer Lowe, Ji Zhou, Omid Mohammadi, Tuomas Puukko, Andreas Albert, Hans Lang, Dieter Ernst, Hannes Kollist, Mikael Brosché, Jörg Durner, Jan Willem Borst, David B. Collinge, Stanisław Karpiński, Michael F. Lyngkjær, Silke Robatzek, Michael Wrzaczek, Jaakko Kangasjärvi , on behalf of the CRK Consortium

A Novel Locus Harbouring a Functional CD164 Nonsense Mutation Identified in a Large Danish Family with Nonsyndromic Hearing Impairment

Mette Nyegaard, Nanna D. Rendtorff, Morten S. Nielsen, Thomas J. Corydon, Ditte Demontis, Anna Starnawska, Anne Hedemand, Annalisa Buniello, Francesco Niola, Michael T. Overgaard, Suzanne M. Leal, Wasim Ahmad, Friedrik P. Wikman, Kirsten B. Petersen, Dorthe G. Crüger, Jaap Oostrik, Hannie Kremer, Niels Tommerup, Morten Frödin, Karen P. Steel, Lisbeth Tranebjærg, Anders D. Børglum

Tempo and Mode of Transposable Element Activity in Drosophila

Robert Kofler, Viola Nolte, Christian Schlötterer

Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers

Christophe Lambing, Kim Osman, Komsun Nuntasoontorn, Allan West, James D. Higgins, Gregory P. Copenhaver, Jianhua Yang, Susan J. Armstrong, Karl Mechtler, Elisabeth Roitinger, F. Chris H. Franklin

Pyrimidine Pool Disequilibrium Induced by a Cytidine Deaminase Deficiency Inhibits PARP-1 Activity, Leading to the Under Replication of DNA

Simon Gemble, Akshay Ahuja, Géraldine Buhagiar-Labarchède, Rosine Onclercq-Delic, Julien Dairou, Denis S. F. Biard, Sarah Lambert, Massimo Lopes, Mounira Amor-Guéret

The SMC Loader Scc2 Promotes ncRNA Biogenesis and Translational Fidelity

Musinu Zakari, Rhonda Trimble Ross, Allison Peak, Marco Blanchette, Chris Seidel, Jennifer L. Gerton

TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements

Kamila Maliszewska-Olejniczak, Julita Gruchota, Robert Gromadka, Cyril Denby Wilkes, Olivier Arnaiz, Nathalie Mathy, Sandra Duharcourt, Mireille Bétermier, Jacek K. Nowak

Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates

Jia-Yu Chen, Qing Sunny Shen, Wei-Zhen Zhou, Jiguang Peng, Bin Z. He, Yumei Li, Chu-Jun Liu, Xuke Luan, Wanqiu Ding, Shuxian Li, Chunyan Chen, Bertrand Chin-Ming Tan, Yong E. Zhang, Aibin He, Chuan-Yun Li

Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process

Toshihiko Kishimoto, Bei-Wen Ying, Saburo Tsuru, Leo Iijima, Shingo Suzuki, Tomomi Hashimoto, Ayana Oyake, Hisaka Kobayashi, Yuki Someya, Dai Narisawa, Tetsuya Yomo

Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools

Jun Ding, Carlo Sidore, Thomas J. Butler, Mary Kate Wing, Yong Qian, Osorio Meirelles, Fabio Busonero, Lam C. Tsoi, Andrea Maschio, Andrea Angius, Hyun Min Kang, Ramaiah Nagaraja, Francesco Cucca, Gonçalo R. Abecasis, David Schlessinger

A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species

Shosei Kubota, Takaya Iwasaki, Kousuke Hanada, Atsushi J. Nagano, Asao Fujiyama, Atsushi Toyoda, Sumio Sugano, Yutaka Suzuki, Kouki Hikosaka, Motomi Ito, Shin-Ichi Morinaga

Identification of a Novel Regulatory Mechanism of Nutrient Transport Controlled by TORC1-Npr1-Amu1/Par32

Mélanie Boeckstaens, Ahmad Merhi, Elisa Llinares, Pascale Van Vooren, Jean-Yves Springael, René Wintjens, Anna Maria Marini

Common Cell Shape Evolution of Two Nasopharyngeal Pathogens

Frédéric J. Veyrier, Nicolas Biais, Pablo Morales, Nouria Belkacem, Cyril Guilhen, Sylvia Ranjeva, Odile Sismeiro, Gérard Péhau-Arnaudet, Eduardo P. Rocha, Catherine Werts, Muhamed-Kheir Taha, Ivo G. Boneca

RFX2 Is a Major Transcriptional Regulator of Spermiogenesis

W. Stephen Kistler, Dominique Baas, Sylvain Lemeille, Marie Paschaki, Queralt Seguin-Estevez, Emmanuèle Barras, Wenli Ma, Jean-Luc Duteyrat, Laurette Morlé, Bénédicte Durand, Walter Reith

AAA-ATPase FIDGETIN-LIKE 1 and Helicase FANCM Antagonize Meiotic Crossovers by Distinct Mechanisms

Chloe Girard, Liudmila Chelysheva, Sandrine Choinard, Nicole Froger, Nicolas Macaisne, Afef Lehmemdi, Julien Mazel, Wayne Crismani, Raphael Mercier

Genetic Evidence for Function of the bHLH-PAS Protein Gce/Met As a Juvenile Hormone Receptor

Marek Jindra, Mirka Uhlirova, Jean-Philippe Charles, Vlastimil Smykal, Ronald J. Hill

Temporal Coordination of Carbohydrate Metabolism during Mosquito Reproduction

Yuan Hou, Xue-Li Wang, Tusar T. Saha, Sourav Roy, Bo Zhao, Alexander S. Raikhel, Zhen Zou

Blimp1/Prdm1 Functions in Opposition to Irf1 to Maintain Neonatal Tolerance during Postnatal Intestinal Maturation

Arne W. Mould, Marc A. J. Morgan, Andrew C. Nelson, Elizabeth K. Bikoff, Elizabeth J. Robertson

Sensory Neurons Arouse C. elegans Locomotion via Both Glutamate and Neuropeptide Release

Seungwon Choi, Kelsey P. Taylor, Marios Chatzigeorgiou, Zhitao Hu, William R. Schafer, Joshua M. Kaplan

Analysis of the Relationships between DNA Double-Strand Breaks, Synaptonemal Complex and Crossovers Using the Atfas1-4 Mutant

Javier Varas, Eugenio Sánchez-Morán, Gregory P. Copenhaver, Juan L. Santos, Mónica Pradillo

In vivo Modeling Implicates APOL1 in Nephropathy: Evidence for Dominant Negative Effects and Epistasis under Anemic Stress

Blair R. Anderson, David N. Howell, Karen Soldano, Melanie E. Garrett, Nicholas Katsanis, Marilyn J. Telen, Erica E. Davis, Allison E. Ashley-Koch

Identification of Chemical Inhibitors of β-Catenin-Driven Liver Tumorigenesis in Zebrafish

Kimberley J. Evason, Macrina T. Francisco, Vladislava Juric, Sanjeev Balakrishnan, Maria del Pilar Lopez Pazmino, John D. Gordan, Sanjay Kakar, Jan Spitsbergen, Andrei Goga, Didier Y. R. Stainier

Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins

Nora Marín-de la Rosa, Anne Pfeiffer, Kristine Hill, Antonella Locascio, Rishikesh P. Bhalerao, Pal Miskolczi, Anne L. Grønlund, Aakriti Wanchoo-Kohli, Stephen G. Thomas, Malcolm J. Bennett, Jan U. Lohmann, Miguel A. Blázquez, David Alabadí

Nutritional Control of DNA Replication Initiation through the Proteolysis and Regulated Translation of DnaA

David J. Leslie, Christian Heinen, Frederic D. Schramm, Marietta Thüring, Christopher D. Aakre, Sean M. Murray, Michael T. Laub, Kristina Jonas

Aurora-A-Dependent Control of TACC3 Influences the Rate of Mitotic Spindle Assembly

Selena G. Burgess, Isabel Peset, Nimesh Joseph, Tommaso Cavazza, Isabelle Vernos, Mark Pfuhl, Fanni Gergely, Richard Bayliss

SAMHD1 Inhibits LINE-1 Retrotransposition by Promoting Stress Granule Formation

Siqi Hu, Jian Li, Fengwen Xu, Shan Mei, Yann Le Duff, Lijuan Yin, Xiaojing Pang, Shan Cen, Qi Jin, Chen Liang, Fei Guo

Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation

Momoko Horikoshi, Reedik Mӓgi, Martijn van de Bunt, Ida Surakka, Antti-Pekka Sarin, Anubha Mahajan, Letizia Marullo, Gudmar Thorleifsson, Sara Hӓgg, Jouke-Jan Hottenga, Claes Ladenvall, Janina S. Ried, Thomas W. Winkler, Sara M. Willems, Natalia Pervjakova, Tõnu Esko, Marian Beekman, Christopher P. Nelson, Christina Willenborg, Steven Wiltshire, Teresa Ferreira, Juan Fernandez, Kyle J. Gaulton, Valgerdur Steinthorsdottir, Anders Hamsten, Patrik K. E. Magnusson, Gonneke Willemsen, Yuri Milaneschi, Neil R. Robertson, Christopher J. Groves, Amanda J. Bennett, Terho Lehtimӓki, Jorma S. Viikari, Johan Rung, Valeriya Lyssenko, Markus Perola, Iris M. Heid, Christian Herder, Harald Grallert, Martina Müller-Nurasyid, Michael Roden, Elina Hypponen, Aaron Isaacs, Elisabeth M. van Leeuwen, Lennart C. Karssen, Evelin Mihailov, Jeanine J. Houwing-Duistermaat, Anton J. M. de Craen, Joris Deelen, Aki S. Havulinna, Matthew Blades, Christian Hengstenberg, Jeanette Erdmann, Heribert Schunkert, Jaakko Kaprio, Martin D. Tobin, Nilesh J. Samani, Lars Lind, Veikko Salomaa, Cecilia M. Lindgren, P. Eline Slagboom, Andres Metspalu, Cornelia M. van Duijn, Johan G. Eriksson, Annette Peters, Christian Gieger, Antti Jula, Leif Groop, Olli T. Raitakari, Chris Power, Brenda W. J. H. Penninx, Eco de Geus, Johannes H. Smit, Dorret I. Boomsma, Nancy L. Pedersen, Erik Ingelsson, Unnur Thorsteinsdottir, Kari Stefansson, Samuli Ripatti, Inga Prokopenko, Mark I. McCarthy, Andrew P. Morris , ENGAGE Consortium

mTOR Directs Breast Morphogenesis through the PKC-alpha-Rac1 Signaling Axis

Meghan M. Morrison, Christian D. Young, Shan Wang, Tammy Sobolik, Violeta M. Sanchez, Donna J. Hicks, Rebecca S. Cook, Dana M. Brantley-Sieders

Reversible Oxidation of a Conserved Methionine in the Nuclear Export Sequence Determines Subcellular Distribution and Activity of the Fungal Nitrate Regulator NirA

Andreas Gallmetzer, Lucia Silvestrini, Thorsten Schinko, Bernd Gesslbauer, Peter Hortschansky, Christoph Dattenböck, María Isabel Muro-Pastor, Andreas Kungl, Axel A. Brakhage, Claudio Scazzocchio, Joseph Strauss

Novel Role for p110β PI 3-Kinase in Male Fertility through Regulation of Androgen Receptor Activity in Sertoli Cells

Julie Guillermet-Guibert, Lee B. Smith, Guillaume Halet, Maria A. Whitehead, Wayne Pearce, Diane Rebourcet, Kelly León, Pascale Crépieux, Gemma Nock, Maria Strömstedt, Malin Enerback, Claude Chelala, Mariona Graupera, John Carroll, Sabina Cosulich, Philippa T. K. Saunders, Ilpo Huhtaniemi, Bart Vanhaesebroeck

Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality

Nicholas C. Wu, C. Anders Olson, Yushen Du, Shuai Le, Kevin Tran, Roland Remenyi, Danyang Gong, Laith Q. Al-Mawsawi, Hangfei Qi, Ting-Ting Wu, Ren Sun

Inference of Low and High-Grade Glioma Gene Regulatory Networks Delineates the Role of Rnd3 in Establishing Multiple Hallmarks of Cancer

Kim Clarke, Thomas Daubon, Nil Turan, Fabienne Soulet, Maihafizah Mohd Zahari, Katie R. Ryan, Sarah Durant, Shan He, John Herbert, John Ankers, John K. Heath, Rolf Bjerkvig, Roy Bicknell, Neil A. Hotchin, Andreas Bikfalvi, Francesco Falciani

Ribosomal Protein Mutations Result in Constitutive p53 Protein Degradation through Impairment of the AKT Pathway

Ana T. Antunes, Yvonne J. Goos, Tamara C. Pereboom, Dorien Hermkens, Marcin W. Wlodarski, Lydie Da Costa, Alyson W. MacInnes

Nmf9 Encodes a Highly Conserved Protein Important to Neurological Function in Mice and Flies

Shuxiao Zhang, Kevin D. Ross, Glen A. Seidner, Michael R. Gorman, Tiffany H. Poon, Xiaobo Wang, Elizabeth M. Keithley, Patricia N. Lee, Mark Q. Martindale, William J. Joiner, Bruce A. Hamilton

TopBP1 Governs Hematopoietic Stem/Progenitor Cells Survival in Zebrafish Definitive Hematopoiesis

Lei Gao, Dantong Li, Ke Ma, Wenjuan Zhang, Tao Xu, Cong Fu, Changbin Jing, Xiaoe Jia, Shuang Wu, Xin Sun, Mei Dong, Min Deng, Yi Chen, Wenge Zhu, Jinrong Peng, Fengyi Wan, Yi Zhou, Leonard I. Zon, Weijun Pan

A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5′ RNA-seq

Sergey Y. Druzhinin, Ngat T. Tran, Kyle S. Skalenko, Seth R. Goldman, Jared G. Knoblauch, Simon L. Dove, Bryce E. Nickels

Cooperation between Paxillin-like Protein Pxl1 and Glucan Synthase Bgs1 Is Essential for Actomyosin Ring Stability and Septum Formation in Fission Yeast

Juan C. G. Cortés, Nuria Pujol, Mamiko Sato, Mario Pinar, Mariona Ramos, Belén Moreno, Masako Osumi, Juan Carlos Ribas, Pilar Pérez