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Table of Contents

February 2018

Cover

Measuring the rate of evolution in hitchhiking Arabidopsis thaliana
Issue Image

Despite its modest appearance and small size, Arabidopsis thaliana has proven to be a successful colonizer. It is found today over much of the United States since its arrival only a few hundred years ago. The species thrives in wild, rural as well as urban settings, and the photo shows an A. thaliana plant thriving in the cracks of a sidewalk. Our study suggests that about four hundred years ago, A. thaliana seeds from a single plant were unknowingly being carried by Europeans to the Eastern US. Who would have guessed that several centuries later, scientists would take advantage of its North American exile, and of pressed plants collected by botanists over the years, to calculate its genomic mutation rate, that is, the speed at which it evolved in the New World? See Exposito-Alonso, Becker et al.

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Image Credit: Moises Exposito-Alonso

Perspectives

Fish mutant, where is thy phenotype?

Darius Balciunas

PLOS Genetics: published February 22, 2018 | https://doi.org/10.1371/journal.pgen.1007197

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Sex: Not all that it’s cracked up to be?

Sebastian Eves-van den Akker, John T. Jones

PLOS Genetics: published February 22, 2018 | https://doi.org/10.1371/journal.pgen.1007160

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Research Articles

Methods for fine-mapping with chromatin and expression data

Megan Roytman, Gleb Kichaev, Alexander Gusev, Bogdan Pasaniuc

PLOS Genetics: published February 26, 2018 | https://doi.org/10.1371/journal.pgen.1007240

Bombyx mori histone methyltransferase BmAsh2 is essential for silkworm piRNA-mediated sex determination

Zhiqian Li, Lang You, Dong Yan, Anthony A. James, Yongping Huang, Anjiang Tan

PLOS Genetics: published February 23, 2018 | https://doi.org/10.1371/journal.pgen.1007245

Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance

Maria Sardi, Vaishnavi Paithane, Michael Place, De Elegant Robinson, James Hose, Dana J. Wohlbach, Audrey P. Gasch

PLOS Genetics: published February 23, 2018 | https://doi.org/10.1371/journal.pgen.1007217

Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC

Xin Bai, Jian-an Jia, Meng Fang, Shipeng Chen, Xiaotao Liang, Shanfeng Zhu, Shuqin Zhang, Jianfeng Feng, Fengzhu Sun, Chunfang Gao

PLOS Genetics: published February 23, 2018 | https://doi.org/10.1371/journal.pgen.1007206

Tissue-specific and mosaic imprinting defects underlie opposite congenital growth disorders in mice

Andrea Freschi, Stella K. Hur, Federica Maria Valente, Folami Y. Ideraabdullah, Angela Sparago, Maria Teresa Gentile, Andrea Oneglia, Diego Di Nucci, Luca Colucci-D’Amato, Joanne L. Thorvaldsen, Marisa S. Bartolomei, Andrea Riccio, Flavia Cerrato

PLOS Genetics: published February 22, 2018 | https://doi.org/10.1371/journal.pgen.1007243

CDK activity provides temporal and quantitative cues for organizing genome duplication

Anthony Perrot, Christopher Lee Millington, Blanca Gómez-Escoda, Diane Schausi-Tiffoche, Pei-Yun Jenny Wu

PLOS Genetics: published February 21, 2018 | https://doi.org/10.1371/journal.pgen.1007214

The COP9 Signalosome regulates seed germination by facilitating protein degradation of RGL2 and ABI5

Dan Jin, Ming Wu, Bosheng Li, Birte Bücker, Philipp Keil, Shaoman Zhang, Jigang Li, Dingming Kang, Jie Liu, Jie Dong, Xing Wang Deng, Vivian Irish, Ning Wei

PLOS Genetics: published February 20, 2018 | https://doi.org/10.1371/journal.pgen.1007237

DNA damage as a consequence of NLR activation

Eleazar Rodriguez, Jonathan Chevalier, Hassan El Ghoul, Kristoffer Voldum-Clausen, John Mundy, Morten Petersen

PLOS Genetics: published February 20, 2018 | https://doi.org/10.1371/journal.pgen.1007235

RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes

Shannel R. Adams, So Maezawa, Kris G. Alavattam, Hironori Abe, Akihiko Sakashita, Megan Shroder, Tyler J. Broering, Julie Sroga Rios, Michael A. Thomas, Xinhua Lin, Carolyn M. Price, Artem Barski, Paul R. Andreassen, Satoshi H. Namekawa

PLOS Genetics: published February 20, 2018 | https://doi.org/10.1371/journal.pgen.1007233

The Mediator co-activator complex regulates Ty1 retromobility by controlling the balance between Ty1i and Ty1 promoters

Alicia C. Salinero, Elisabeth R. Knoll, Z. Iris Zhu, David Landsman, M. Joan Curcio, Randall H. Morse

PLOS Genetics: published February 20, 2018 | https://doi.org/10.1371/journal.pgen.1007232

The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation

Sean L. Beckwith, Erin K. Schwartz, Pablo E. García-Nieto, Devin A. King, Graeme J. Gowans, Ka Man Wong, Tessa L. Eckley, Alexander P. Paraschuk, Egan L. Peltan, Laura R. Lee, Wei Yao, Ashby J. Morrison

PLOS Genetics: published February 20, 2018 | https://doi.org/10.1371/journal.pgen.1007216

Brca2, Pds5 and Wapl differentially control cohesin chromosome association and function

Ziva Misulovin, Michelle Pherson, Maria Gause, Dale Dorsett

PLOS Genetics: published February 15, 2018 | https://doi.org/10.1371/journal.pgen.1007225

Early experiences mediate distinct adult gene expression and reproductive programs in Caenorhabditis elegans

Maria C. Ow, Kirill Borziak, Alexandra M. Nichitean, Steve Dorus, Sarah E. Hall

PLOS Genetics: published February 15, 2018 | https://doi.org/10.1371/journal.pgen.1007219

A molecular basis behind heterophylly in an amphibious plant, Ranunculus trichophyllus

Juhyun Kim, Youngsung Joo, Jinseul Kyung, Myeongjune Jeon, Jong Yoon Park, Ho Gyun Lee, Doo Soo Chung, Eunju Lee, Ilha Lee

PLOS Genetics: published February 15, 2018 | https://doi.org/10.1371/journal.pgen.1007208

Paternal lineage early onset hereditary ovarian cancers: A Familial Ovarian Cancer Registry study

Kevin H. Eng, J. Brian Szender, John Lewis Etter, Jasmine Kaur, Samantha Poblete, Ruea-Yea Huang, Qianqian Zhu, Katherine A. Grzesik, Sebastiano Battaglia, Rikki Cannioto, John J. Krolewski, Emese Zsiros, Peter J. Frederick, Shashikant B. Lele, Kirsten B. Moysich, Kunle O. Odunsi

PLOS Genetics: published February 15, 2018 | https://doi.org/10.1371/journal.pgen.1007194

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The PHD finger protein Spp1 has distinct functions in the Set1 and the meiotic DSB formation complexes

Céline Adam, Raphaël Guérois, Anna Citarella, Laura Verardi, Florine Adolphe, Claire Béneut, Vérane Sommermeyer, Claire Ramus, Jérôme Govin, Yohann Couté, Valérie Borde

PLOS Genetics: published February 14, 2018 | https://doi.org/10.1371/journal.pgen.1007223

Peculiar combinations of individually non-pathogenic missense mitochondrial DNA variants cause low penetrance Leber’s hereditary optic neuropathy

Leonardo Caporali, Luisa Iommarini, Chiara La Morgia, Anna Olivieri, Alessandro Achilli, Alessandra Maresca, Maria Lucia Valentino, Mariantonietta Capristo, Francesca Tagliavini, Valentina Del Dotto, Claudia Zanna, Rocco Liguori, Piero Barboni, Michele Carbonelli, Veronica Cocetta, Monica Montopoli, Andrea Martinuzzi, Giovanna Cenacchi, Giuseppe De Michele, Francesco Testa, Anna Nesti, Francesca Simonelli, Anna Maria Porcelli, Antonio Torroni, Valerio Carelli

PLOS Genetics: published February 14, 2018 | https://doi.org/10.1371/journal.pgen.1007210

EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum

Seijiro Ono, Hua Liu, Katsutoshi Tsuda, Eigo Fukai, Keisuke Tanaka, Takuji Sasaki, Ken-Ichi Nonomura

PLOS Genetics: published February 12, 2018 | https://doi.org/10.1371/journal.pgen.1007238

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SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs

Daniel W. Hagey, Susanne Klum, Idha Kurtsdotter, Cecile Zaouter, Danijal Topcic, Olov Andersson, Maria Bergsland, Jonas Muhr

PLOS Genetics: published February 12, 2018 | https://doi.org/10.1371/journal.pgen.1007224

Comprehensive analysis of central carbon metabolism illuminates connections between nutrient availability, growth rate, and cell morphology in Escherichia coli

Corey S. Westfall, Petra Anne Levin

PLOS Genetics: published February 12, 2018 | https://doi.org/10.1371/journal.pgen.1007205

The rate and potential relevance of new mutations in a colonizing plant lineage

Moises Exposito-Alonso, Claude Becker, Verena J. Schuenemann, Ella Reiter, Claudia Setzer, Radka Slovak, Benjamin Brachi, Jörg Hagmann, Dominik G. Grimm, Jiahui Chen, Wolfgang Busch, Joy Bergelson, Rob W. Ness, Johannes Krause, Hernán A. Burbano, Detlef Weigel

PLOS Genetics: published February 12, 2018 | https://doi.org/10.1371/journal.pgen.1007155

An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations

Arunabha Majumdar, Tanushree Haldar, Sourabh Bhattacharya, John S. Witte

PLOS Genetics: published February 12, 2018 | https://doi.org/10.1371/journal.pgen.1007139

Drosophila PLP assembles pericentriolar clouds that promote centriole stability, cohesion and MT nucleation

Helio Roque, Saroj Saurya, Metta B. Pratt, Errin Johnson, Jordan W. Raff

PLOS Genetics: published February 9, 2018 | https://doi.org/10.1371/journal.pgen.1007198

Drosophila Gr64e mediates fatty acid sensing via the phospholipase C pathway

Hyeyon Kim, Haein Kim, Jae Young Kwon, Jeong Taeg Seo, Dong Min Shin, Seok Jun Moon

PLOS Genetics: published February 8, 2018 | https://doi.org/10.1371/journal.pgen.1007229

Genetic compensation triggered by actin mutation prevents the muscle damage caused by loss of actin protein

Tamar E. Sztal, Emily A. McKaige, Caitlin Williams, Avnika A. Ruparelia, Robert J. Bryson-Richardson

PLOS Genetics: published February 8, 2018 | https://doi.org/10.1371/journal.pgen.1007212

Th-POK regulates mammary gland lactation through mTOR-SREBP pathway

Rui Zhang, Huimin Ma, Yuan Gao, Yanjun Wu, Yuemei Qiao, Ajun Geng, Cheguo Cai, Yingying Han, Yi Arial Zeng, Xiaolong Liu, Gaoxiang Ge

PLOS Genetics: published February 8, 2018 | https://doi.org/10.1371/journal.pgen.1007211

An alternatively spliced form affecting the Marked Box domain of Drosophila E2F1 is required for proper cell cycle regulation

Minhee Kim, Jack P. Tang, Nam-Sung Moon

PLOS Genetics: published February 8, 2018 | https://doi.org/10.1371/journal.pgen.1007204

Differential roles of the Drosophila EMT-inducing transcription factors Snail and Serpent in driving primary tumour growth

Kyra Campbell, Gaëlle Lebreton, Xavier Franch-Marro, Jordi Casanova

PLOS Genetics: published February 8, 2018 | https://doi.org/10.1371/journal.pgen.1007167

Rictor/TORC2 mediates gut-to-brain signaling in the regulation of phenotypic plasticity in C. elegans

Michael P. O’Donnell, Pin-Hao Chao, Jan E. Kammenga, Piali Sengupta

PLOS Genetics: published February 7, 2018 | https://doi.org/10.1371/journal.pgen.1007213

Gli3 is a negative regulator of Tas1r3-expressing taste cells

Yumei Qin, Sunil K. Sukumaran, Masafumi Jyotaki, Kevin Redding, Peihua Jiang, Robert F. Margolskee

PLOS Genetics: published February 7, 2018 | https://doi.org/10.1371/journal.pgen.1007058

Axin phosphorylation in both Wnt-off and Wnt-on states requires the tumor suppressor APC

Ofelia Tacchelly-Benites, Zhenghan Wang, Eungi Yang, Hassina Benchabane, Ai Tian, Michael P. Randall, Yashi Ahmed

PLOS Genetics: published February 6, 2018 | https://doi.org/10.1371/journal.pgen.1007178

STERILE APETALA modulates the stability of a repressor protein complex to control organ size in Arabidopsis thaliana

Na Li, Zupei Liu, Zhibiao Wang, Licong Ru, Nathalie Gonzalez, Alexandra Baekelandt, Laurens Pauwels, Alain Goossens, Ran Xu, Zhengge Zhu, Dirk Inzé, Yunhai Li

PLOS Genetics: published February 5, 2018 | https://doi.org/10.1371/journal.pgen.1007218

Ras/ERK-signalling promotes tRNA synthesis and growth via the RNA polymerase III repressor Maf1 in Drosophila

Shrivani Sriskanthadevan-Pirahas, Rujuta Deshpande, Byoungchun Lee, Savraj S. Grewal

PLOS Genetics: published February 5, 2018 | https://doi.org/10.1371/journal.pgen.1007202

Sem1 links proteasome stability and specificity to multicellular development

Miriam Kolog Gulko, Gabriele Heinrich, Carina Gross, Blagovesta Popova, Oliver Valerius, Piotr Neumann, Ralf Ficner, Gerhard H. Braus

PLOS Genetics: published February 5, 2018 | https://doi.org/10.1371/journal.pgen.1007141

Nuclear re-localization of Dicer in primary mouse embryonic fibroblast nuclei following DNA damage

Kaspar Burger, Monika Gullerova

PLOS Genetics: published February 2, 2018 | https://doi.org/10.1371/journal.pgen.1007151

Chinmo prevents transformer alternative splicing to maintain male sex identity

Lydia Grmai, Bruno Hudry, Irene Miguel-Aliaga, Erika A. Bach

PLOS Genetics: published February 1, 2018 | https://doi.org/10.1371/journal.pgen.1007203

Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk

Rosalie G. Waller, Todd M. Darlington, Xiaomu Wei, Michael J. Madsen, Alun Thomas, Karen Curtin, Hilary Coon, Venkatesh Rajamanickam, Justin Musinsky, David Jayabalan, Djordje Atanackovic, S. Vincent Rajkumar, Shaji Kumar, Susan Slager, Mridu Middha, Perrine Galia, Delphine Demangel, Mohamed Salama, Vijai Joseph, James McKay, Kenneth Offit, Robert J. Klein, Steven M. Lipkin, Charles Dumontet, Celine M. Vachon, Nicola J. Camp

PLOS Genetics: published February 1, 2018 | https://doi.org/10.1371/journal.pgen.1007111