May 2013

This montage shows a time-lapse of the C. elegans spermatheca, the site of sperm storage and fertilization, imaged with the genetically encoded calcium indicator GCaMP. Oocyte entry into the spermatheca stretches the spermathecal cells and initiates a series of calcium waves that sweep across the spermatheca and trigger myosin contractions, which propel the embryo into the uterus. In this image, the calcium oscillations are visible as brightening and dimming of the distal and proximal spermatheca. The authors show that FLN-1/filamin, a mechanically sensitive cytoskeletal protein, and PLC-1, a phospholipase, are key regulators of this process. See Kovacevic et al.

Image Credit: Dr. Erin Cram and Dr. Ismar Kovacevic

Perspectives

Side Effects: Substantial Non-Neutral Evolution Flanking Regulatory Sites

James G. D. Prendergast, Colin A. Semple

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003528

From Paramutation to Paradigm

Ian R. Adams, Richard R. Meehan

PLOS Genetics: published May 23, 2013 | https://doi.org/10.1371/journal.pgen.1003537

Review

Global Properties and Functional Complexity of Human Gene Regulatory Variation

Daniel J. Gaffney

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003501

Research Articles

Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences

Ephraim Kenigsberg, Amos Tanay

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003512

Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits

Noah Zaitlen, Peter Kraft, Nick Patterson, Bogdan Pasaniuc, Gaurav Bhatia, Samuela Pollack, Alkes L. Price

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003520

Strong Purifying Selection at Synonymous Sites in D. melanogaster

David S. Lawrie, Philipp W. Messer, Ruth Hershberg, Dmitri A. Petrov

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003527

GLIS3, a Susceptibility Gene for Type 1 and Type 2 Diabetes, Modulates Pancreatic Beta Cell Apoptosis via Regulation of a Splice Variant of the BH3-Only Protein Bim

Tatiane C. Nogueira, Flavia M. Paula, Olatz Villate, Maikel L. Colli, Rodrigo F. Moura, Daniel A. Cunha, Lorella Marselli, Piero Marchetti, Miriam Cnop, Cécile Julier, Decio L. Eizirik

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003532

Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis thaliana

Hirokazu Tanaka, Saeko Kitakura, Hana Rakusová, Tomohiro Uemura, Mugurel I. Feraru, Riet De Rycke, Stéphanie Robert, Tatsuo Kakimoto, Jiří Friml

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003540

DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria

Antonella Fioravanti, Coralie Fumeaux, Saswat S. Mohapatra, Coralie Bompard, Matteo Brilli, Antonio Frandi, Vincent Castric, Vincent Villeret, Patrick H. Viollier, Emanuele G. Biondi

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003541

CDK4 T172 Phosphorylation Is Central in a CDK7-Dependent Bidirectional CDK4/CDK2 Interplay Mediated by p21 Phosphorylation at the Restriction Point

Xavier Bisteau, Sabine Paternot, Bianca Colleoni, Karin Ecker, Katia Coulonval, Philippe De Groote, Wim Declercq, Ludger Hengst, Pierre P. Roger

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003546

Interactions with Iridophores and the Tissue Environment Required for Patterning Melanophores and Xanthophores during Zebrafish Adult Pigment Stripe Formation

Larissa B. Patterson, David M. Parichy

PLOS Genetics: published May 30, 2013 | https://doi.org/10.1371/journal.pgen.1003561

Analysis of the Genetic Basis of Disease in the Context of Worldwide Human Relationships and Migration

Erik Corona, Rong Chen, Martin Sikora, Alexander A. Morgan, Chirag J. Patel, Aditya Ramesh, Carlos D. Bustamante, Atul J. Butte

PLOS Genetics: published May 23, 2013 | https://doi.org/10.1371/journal.pgen.1003447

RNA–Mediated Epigenetic Heredity Requires the Cytosine Methyltransferase Dnmt2

Jafar Kiani, Valérie Grandjean, Reinhard Liebers, Francesca Tuorto, Hossein Ghanbarian, Frank Lyko, François Cuzin, Minoo Rassoulzadegan

PLOS Genetics: published May 23, 2013 | https://doi.org/10.1371/journal.pgen.1003498

Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations

Gavin Band, Quang Si Le, Luke Jostins, Matti Pirinen, Katja Kivinen, Muminatou Jallow, Fatoumatta Sisay-Joof, Kalifa Bojang, Margaret Pinder, Giorgio Sirugo, David J. Conway, Vysaul Nyirongo, David Kachala, Malcolm Molyneux, Terrie Taylor, Carolyne Ndila, Norbert Peshu, Kevin Marsh, Thomas N. Williams, Daniel Alcock, Robert Andrews, Sarah Edkins, Emma Gray, Christina Hubbart, Anna Jeffreys, Kate Rowlands, Kathrin Schuldt, Taane G. Clark, Kerrin S. Small, Yik Ying Teo, Dominic P. Kwiatkowski, Kirk A. Rockett, Jeffrey C. Barrett, Chris C. A. Spencer, Malaria Genomic Epidemiological Network ¶

PLOS Genetics: published May 23, 2013 | https://doi.org/10.1371/journal.pgen.1003509

Ikbkap/Elp1 Deficiency Causes Male Infertility by Disrupting Meiotic Progression

Fu-Jung Lin, Li Shen, Chuan-Wei Jang, Pål Ø. Falnes, Yi Zhang

PLOS Genetics: published May 23, 2013 | https://doi.org/10.1371/journal.pgen.1003516

ttm-1 Encodes CDF Transporters That Excrete Zinc from Intestinal Cells of C. elegans and Act in a Parallel Negative Feedback Circuit That Promotes Homeostasis

Hyun Cheol Roh, Sara Collier, Krupa Deshmukh, James Guthrie, J. David Robertson, Kerry Kornfeld

PLOS Genetics: published May 23, 2013 | https://doi.org/10.1371/journal.pgen.1003522

Arabidopsis thaliana RESISTANCE TO FUSARIUM OXYSPORUM 2 Implicates Tyrosine-Sulfated Peptide Signaling in Susceptibility and Resistance to Root Infection

Yunping Shen, Andrew C. Diener

PLOS Genetics: published May 23, 2013 | https://doi.org/10.1371/journal.pgen.1003525

Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway

Gang Li, Dorothée Diogo, Di Wu, Jim Spoonamore, Vlado Dancik, Lude Franke, Fina Kurreeman, Elizabeth J. Rossin, Grant Duclos, Cathy Hartland, Xuezhong Zhou, Kejie Li, Jun Liu, Philip L. De Jager, Katherine A. Siminovitch, Alexandra Zhernakova, Soumya Raychaudhuri, John Bowes, Steve Eyre, Leonid Padyukov, Peter K. Gregersen, Jane Worthington, Rheumatoid Arthritis Consortium International (RACI), Namrata Gupta, Paul A. Clemons, Eli Stahl, Nicola Tolliday, Robert M. Plenge

PLOS Genetics: published May 16, 2013 | https://doi.org/10.1371/journal.pgen.1003487

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

Gaurav Dugar, Alexander Herbig, Konrad U. Förstner, Nadja Heidrich, Richard Reinhardt, Kay Nieselt, Cynthia M. Sharma

PLOS Genetics: published May 16, 2013 | https://doi.org/10.1371/journal.pgen.1003495

Congruence of Additive and Non-Additive Effects on Gene Expression Estimated from Pedigree and SNP Data

Joseph E. Powell, Anjali K. Henders, Allan F. McRae, Jinhee Kim, Gibran Hemani, Nicholas G. Martin, Emmanouil T. Dermitzakis, Greg Gibson, Grant W. Montgomery, Peter M. Visscher

PLOS Genetics: published May 16, 2013 | https://doi.org/10.1371/journal.pgen.1003502

HDAC7 Is a Repressor of Myeloid Genes Whose Downregulation Is Required for Transdifferentiation of Pre-B Cells into Macrophages

Bruna Barneda-Zahonero, Lidia Román-González, Olga Collazo, Haleh Rafati, Abul B. M. M. K. Islam, Lars H. Bussmann, Alessandro di Tullio, Luisa De Andres, Thomas Graf, Núria López-Bigas, Tokameh Mahmoudi, Maribel Parra

PLOS Genetics: published May 16, 2013 | https://doi.org/10.1371/journal.pgen.1003503

ATM–Dependent MiR-335 Targets CtIP and Modulates the DNA Damage Response

Nathan T. Martin, Kotoka Nakamura, Robert Davies, Shareef A. Nahas, Christina Brown, Rashmi Tunuguntla, Richard A. Gatti, Hailiang Hu

PLOS Genetics: published May 16, 2013 | https://doi.org/10.1371/journal.pgen.1003505

The Secretory Pathway Calcium ATPase PMR-1/SPCA1 Has Essential Roles in Cell Migration during Caenorhabditis elegans Embryonic Development

Vida Praitis, Jeffrey Simske, Sarah Kniss, Rebecca Mandt, Leah Imlay, Charlotte Feddersen, Michael B. Miller, Juliet Mushi, Walter Liszewski, Rachel Weinstein, Adityarup Chakravorty, Dae-Gon Ha, Angela Schacht Farrell, Alexander Sullivan-Wilson, Tyson Stock

PLOS Genetics: published May 16, 2013 | https://doi.org/10.1371/journal.pgen.1003506

Clathrin and AP2 Are Required for Phagocytic Receptor-Mediated Apoptotic Cell Clearance in Caenorhabditis elegans

Didi Chen, Youli Jian, Xuezhao Liu, Yuanya Zhang, Jingjing Liang, Xiaying Qi, Hongwei Du, Wei Zou, Lianwan Chen, Yongping Chai, Guangshuo Ou, Long Miao, Yingchun Wang, Chonglin Yang

PLOS Genetics: published May 16, 2013 | https://doi.org/10.1371/journal.pgen.1003517

Duplication and Retention Biases of Essential and Non-Essential Genes Revealed by Systematic Knockdown Analyses

Shane Woods, Avril Coghlan, David Rivers, Tobias Warnecke, Sean J. Jeffries, Taejoon Kwon, Anthony Rogers, Laurence D. Hurst, Julie Ahringer

PLOS Genetics: published May 9, 2013 | https://doi.org/10.1371/journal.pgen.1003330

Genome-Wide Analysis in German Shepherd Dogs Reveals Association of a Locus on CFA 27 with Atopic Dermatitis

Katarina Tengvall, Marcin Kierczak, Kerstin Bergvall, Mia Olsson, Marcel Frankowiack, Fabiana H. G. Farias, Gerli Pielberg, Örjan Carlborg, Tosso Leeb, Göran Andersson, Lennart Hammarström, Åke Hedhammar, Kerstin Lindblad-Toh

PLOS Genetics: published May 9, 2013 | https://doi.org/10.1371/journal.pgen.1003475

The Genomic Signature of Crop-Wild Introgression in Maize

Matthew B. Hufford, Pesach Lubinksy, Tanja Pyhäjärvi, Michael T. Devengenzo, Norman C. Ellstrand, Jeffrey Ross-Ibarra

PLOS Genetics: published May 9, 2013 | https://doi.org/10.1371/journal.pgen.1003477

Liver X Receptors Protect from Development of Prostatic Intra-Epithelial Neoplasia in Mice

Aurélien J. C. Pommier, Julie Dufour, Georges Alves, Emilie Viennois, Hugues De Boussac, Amalia Trousson, David H. Volle, Françoise Caira, Pierre Val, Philippe Arnaud, Jean-Marc A. Lobaccaro, Silvère Baron

PLOS Genetics: published May 9, 2013 | https://doi.org/10.1371/journal.pgen.1003483

From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes

Benjamin Georgi, Benjamin F. Voight, Maja Bućan

PLOS Genetics: published May 9, 2013 | https://doi.org/10.1371/journal.pgen.1003484

A Statistical Framework for Joint eQTL Analysis in Multiple Tissues

Timothée Flutre, Xiaoquan Wen, Jonathan Pritchard, Matthew Stephens

PLOS Genetics: published May 9, 2013 | https://doi.org/10.1371/journal.pgen.1003486

Loss of Expression and Promoter Methylation of SLIT2 Are Associated with Sessile Serrated Adenoma Formation

Andrew D. Beggs, Angela Jones, Neil Shepherd, Abed Arnaout, Caroline Finlayson, A. Muti Abulafi, Dion G. Morton, Glenn M. Matthews, Shirley V. Hodgson, Ian P. M. Tomlinson

PLOS Genetics: published May 9, 2013 | https://doi.org/10.1371/journal.pgen.1003488

Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

Olga A. Soutourina, Marc Monot, Pierre Boudry, Laure Saujet, Christophe Pichon, Odile Sismeiro, Ekaterina Semenova, Konstantin Severinov, Chantal Le Bouguenec, Jean-Yves Coppée, Bruno Dupuy, Isabelle Martin-Verstraete

PLOS Genetics: published May 9, 2013 | https://doi.org/10.1371/journal.pgen.1003493

Chromosome Movements Promoted by the Mitochondrial Protein SPD-3 Are Required for Homology Search during Caenorhabditis elegans Meiosis

Leticia Labrador, Consuelo Barroso, James Lightfoot, Thomas Müller-Reichert, Stephane Flibotte, Jon Taylor, Donald G. Moerman, Anne M. Villeneuve, Enrique Martinez-Perez

PLOS Genetics: published May 9, 2013 | https://doi.org/10.1371/journal.pgen.1003497

Cover

Time-lapse of the spermatheca in a nematode worm

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