January 2018

False colored SEM image of an Arabidopsis mutant fruit showing ovules transformed into flower organ-like structure (green) or finger-like protrusion (purple). A wild-type developing ovule appears in orange. Ovule identity is conferred by homeotic D-class genes SHATTERPROOF1 (SHP1), SHP2 and SEEDSTICK (STK), related to the MADS-domain gene AGAMOUS (AG). AG pre-mRNA maturation is regulated by RNA-binding protein-encoding genes collectively termed the HUA-PEP activity. SHP1, SHP2 and STK activity is dramatically reduced in severe hua-pep backgrounds. Prematurely terminated transcripts accumulate at the expense of functional transcripts, pointing to pre-mRNA processing misregulation as the origin of the ovule developmental defects. See Rodríguez-Cazorla et al.

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Image Credit: E. Rodríguez-Cazorla, A. Martínez-Laborda, A. Vera

Reviews

Taking cohesin and condensin in context

Kobe C. Yuen, Jennifer L. Gerton

PLOS Genetics: published January 25, 2018 | https://doi.org/10.1371/journal.pgen.1007118

Aging and the rise of somatic cancer-associated mutations in normal tissues

Rosa Ana Risques, Scott R. Kennedy

PLOS Genetics: published January 4, 2018 | https://doi.org/10.1371/journal.pgen.1007108

Research Articles

Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

Rohan Maddamsetti, Richard E. Lenski

PLOS Genetics: published January 31, 2018 | https://doi.org/10.1371/journal.pgen.1007199

Inferring sex-specific demographic history from SNP data

Florian Clemente, Mathieu Gautier, Renaud Vitalis

PLOS Genetics: published January 31, 2018 | https://doi.org/10.1371/journal.pgen.1007191

Coordination of olfactory receptor choice with guidance receptor expression and function in olfactory sensory neurons

Puneet Dang, Stephen A. Fisher, Derek J. Stefanik, Junhyong Kim, Jonathan A. Raper

PLOS Genetics: published January 31, 2018 | https://doi.org/10.1371/journal.pgen.1007164

Rasa3 controls turnover of endothelial cell adhesion and vascular lumen integrity by a Rap1-dependent mechanism

Patricia Molina-Ortiz, Tanguy Orban, Maud Martin, Audrey Habets, Franck Dequiedt, Stéphane Schurmans

PLOS Genetics: published January 30, 2018 | https://doi.org/10.1371/journal.pgen.1007195

MGA, L3MBTL2 and E2F6 determine genomic binding of the non-canonical Polycomb repressive complex PRC1.6

Bastian Stielow, Florian Finkernagel, Thorsten Stiewe, Andrea Nist, Guntram Suske

PLOS Genetics: published January 30, 2018 | https://doi.org/10.1371/journal.pgen.1007193

Novel genetic polymorphisms associated with severe malaria and under selective pressure in North-eastern Tanzania

Matt Ravenhall, Susana Campino, Nuno Sepúlveda, Alphaxard Manjurano, Behzad Nadjm, George Mtove, Hannah Wangai, Caroline Maxwell, Raimos Olomi, Hugh Reyburn, Christopher J. Drakeley, Eleanor M. Riley, Taane G. Clark, in collaboration with MalariaGEN

PLOS Genetics: published January 30, 2018 | https://doi.org/10.1371/journal.pgen.1007172

The non-classical nuclear import carrier Transportin 1 modulates circadian rhythms through its effect on PER1 nuclear localization

Sandra Korge, Bert Maier, Franziska Brüning, Lea Ehrhardt, Thomas Korte, Matthias Mann, Andreas Herrmann, Maria S. Robles, Achim Kramer

PLOS Genetics: published January 29, 2018 | https://doi.org/10.1371/journal.pgen.1007189

Identifying and exploiting trait-relevant tissues with multiple functional annotations in genome-wide association studies

Xingjie Hao, Ping Zeng, Shujun Zhang, Xiang Zhou

PLOS Genetics: published January 29, 2018 | https://doi.org/10.1371/journal.pgen.1007186

Rewired RNAi-mediated genome surveillance in house dust mites

Mosharrof Mondal, Pavel Klimov, Alex Sutton Flynt

PLOS Genetics: published January 29, 2018 | https://doi.org/10.1371/journal.pgen.1007183

Transcriptional regulatory control of mammalian nephron progenitors revealed by multi-factor cistromic analysis and genetic studies

Lori L. O’Brien, Qiuyu Guo, Emad Bahrami-Samani, Joo-Seop Park, Sean M. Hasso, Young-Jin Lee, Alan Fang, Albert D. Kim, Jinjin Guo, Trudy M. Hong, Kevin A. Peterson, Scott Lozanoff, Ramya Raviram, Bing Ren, Ben Fogelgren, Andrew D. Smith, Anton Valouev, Andrew P. McMahon

PLOS Genetics: published January 29, 2018 | https://doi.org/10.1371/journal.pgen.1007181

WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity

Tomáš Prát, Jakub Hajný, Wim Grunewald, Mina Vasileva, Gergely Molnár, Ricardo Tejos, Markus Schmid, Michael Sauer, Jiří Friml

PLOS Genetics: published January 29, 2018 | https://doi.org/10.1371/journal.pgen.1007177

Kinesin Khc-73/KIF13B modulates retrograde BMP signaling by influencing endosomal dynamics at the Drosophila neuromuscular junction

Edward H. Liao, Lindsay Gray, Kazuya Tsurudome, Wassim El-Mounzer, Fatima Elazzouzi, Christopher Baim, Sarah Farzin, Mario R. Calderon, Grant Kauwe, A. Pejmun Haghighi

PLOS Genetics: published January 26, 2018 | https://doi.org/10.1371/journal.pgen.1007184

CRL4 antagonizes SCF^Fbxo7-mediated turnover of cereblon and BK channel to regulate learning and memory

Tianyu Song, Shenghui Liang, Jiye Liu, Tingyue Zhang, Yifei Yin, Chenlu Geng, Shaobing Gao, Yan Feng, Hao Xu, Dongqing Guo, Amanda Roberts, Yuchun Gu, Yong Cang

PLOS Genetics: published January 25, 2018 | https://doi.org/10.1371/journal.pgen.1007165

A switch in the mode of Wnt signaling orchestrates the formation of germline stem cell differentiation niche in Drosophila

Maitreyi Upadhyay, Michael Kuna, Sara Tudor, Yesenia Martino Cortez, Prashanth Rangan

PLOS Genetics: published January 25, 2018 | https://doi.org/10.1371/journal.pgen.1007154

Insular Celtic population structure and genomic footprints of migration

Ross P. Byrne, Rui Martiniano, Lara M. Cassidy, Matthew Carrigan, Garrett Hellenthal, Orla Hardiman, Daniel G. Bradley, Russell L. McLaughlin

PLOS Genetics: published January 25, 2018 | https://doi.org/10.1371/journal.pgen.1007152

Genomic locus modulating corneal thickness in the mouse identifies POU6F2 as a potential risk of developing glaucoma

Rebecca King, Felix L. Struebing, Ying Li, Jiaxing Wang, Allison Ashley Koch, Jessica N. Cooke Bailey, Puya Gharahkhani, International Glaucoma Genetics Consortium, NEIGHBORHOOD Consortium, Stuart MacGregor, R. Rand Allingham, Michael A. Hauser, Janey L. Wiggs, Eldon E. Geisert

PLOS Genetics: published January 25, 2018 | https://doi.org/10.1371/journal.pgen.1007145

HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression

Alix Warburton, Catherine J. Redmond, Katharine E. Dooley, Haiqing Fu, Maura L. Gillison, Keiko Akagi, David E. Symer, Mirit I. Aladjem, Alison A. McBride

PLOS Genetics: published January 24, 2018 | https://doi.org/10.1371/journal.pgen.1007179

Mutations in THAP1/DYT6 reveal that diverse dystonia genes disrupt similar neuronal pathways and functions

Zuchra Zakirova, Tomas Fanutza, Justine Bonet, Ben Readhead, Weijia Zhang, Zhengzi Yi, Genevieve Beauvais, Thomas P. Zwaka, Laurie J. Ozelius, Robert D. Blitzer, Pedro Gonzalez-Alegre, Michelle E. Ehrlich

PLOS Genetics: published January 24, 2018 | https://doi.org/10.1371/journal.pgen.1007169

Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity

Montserrat Torres-Oliva, Julia Schneider, Gordon Wiegleb, Felix Kaufholz, Nico Posnien

PLOS Genetics: published January 23, 2018 | https://doi.org/10.1371/journal.pgen.1007180

Acute Smc5/6 depletion reveals its primary role in rDNA replication by restraining recombination at fork pausing sites

Xiao P. Peng, Shelly Lim, Shibai Li, Lisette Marjavaara, Andrei Chabes, Xiaolan Zhao

PLOS Genetics: published January 23, 2018 | https://doi.org/10.1371/journal.pgen.1007129

Knockdown of wfs1, a fly homolog of Wolfram syndrome 1, in the nervous system increases susceptibility to age- and stress-induced neuronal dysfunction and degeneration in Drosophila

Yasufumi Sakakibara, Michiko Sekiya, Naoki Fujisaki, Xiuming Quan, Koichi M. Iijima

PLOS Genetics: published January 22, 2018 | https://doi.org/10.1371/journal.pgen.1007196

Signalling crosstalk during early tumorigenesis in the absence of Polycomb silencing

Jorge V. Beira, Joana Torres, Renato Paro

PLOS Genetics: published January 22, 2018 | https://doi.org/10.1371/journal.pgen.1007187

Genetic variants in pachyonychia congenita-associated keratins increase susceptibility to tooth decay

Olivier Duverger, Jenna C. Carlson, Chelsea M. Karacz, Mary E. Schwartz, Michael A. Cross, Mary L. Marazita, John R. Shaffer, Maria I. Morasso

PLOS Genetics: published January 22, 2018 | https://doi.org/10.1371/journal.pgen.1007168

Repression of branched-chain amino acid synthesis in Staphylococcus aureus is mediated by isoleucine via CodY, and by a leucine-rich attenuator peptide

Julienne C. Kaiser, Alyssa N. King, Jason C. Grigg, Jessica R. Sheldon, David R. Edgell, Michael E. P. Murphy, Shaun R. Brinsmade, David E. Heinrichs

PLOS Genetics: published January 22, 2018 | https://doi.org/10.1371/journal.pgen.1007159

The Arabidopsis SUMO E3 ligase SIZ1 mediates the temperature dependent trade-off between plant immunity and growth

Valentin Hammoudi, Like Fokkens, Bas Beerens, Georgios Vlachakis, Sayantani Chatterjee, Manuel Arroyo-Mateos, Paul F. K. Wackers, Martijs J. Jonker, Harrold A. van den Burg

PLOS Genetics: published January 22, 2018 | https://doi.org/10.1371/journal.pgen.1007157

Compound heterozygous loss-of-function mutations in KIF20A are associated with a novel lethal congenital cardiomyopathy in two siblings

Jacoba J. Louw, Ricardo Nunes Bastos, Xiaowen Chen, Céline Verdood, Anniek Corveleyn, Yaojuan Jia, Jeroen Breckpot, Marc Gewillig, Hilde Peeters, Massimo M. Santoro, Francis Barr, Koenraad Devriendt

PLOS Genetics: published January 22, 2018 | https://doi.org/10.1371/journal.pgen.1007138

A HAD family phosphatase CSP-6 regulates the circadian output pathway in Neurospora crassa

Xiaoying Zhou, Bin Wang, Jillian M. Emerson, Carol S. Ringelberg, Scott A. Gerber, Jennifer J. Loros, Jay C. Dunlap

PLOS Genetics: published January 19, 2018 | https://doi.org/10.1371/journal.pgen.1007192

Allocation of distinct organ fates from a precursor field requires a shift in expression and function of gene regulatory networks

Sneha Palliyil, Jinjin Zhu, Luke R. Baker, Sarah D. Neuman, Arash Bashirullah, Justin P. Kumar

PLOS Genetics: published January 19, 2018 | https://doi.org/10.1371/journal.pgen.1007185

DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli

Sarah S. Henrikus, Elizabeth A. Wood, John P. McDonald, Michael M. Cox, Roger Woodgate, Myron F. Goodman, Antoine M. van Oijen, Andrew Robinson

PLOS Genetics: published January 19, 2018 | https://doi.org/10.1371/journal.pgen.1007161

Histological subtypes of mouse mammary tumors reveal conserved relationships to human cancers

Daniel P. Hollern, Matthew R. Swiatnicki, Eran R. Andrechek

PLOS Genetics: published January 18, 2018 | https://doi.org/10.1371/journal.pgen.1007135

6-OHDA-induced dopaminergic neurodegeneration in Caenorhabditis elegans is promoted by the engulfment pathway and inhibited by the transthyretin-related protein TTR-33

Sarah-Lena Offenburger, Xue Yan Ho, Theresa Tachie-Menson, Sean Coakley, Massimo A. Hilliard, Anton Gartner

PLOS Genetics: published January 18, 2018 | https://doi.org/10.1371/journal.pgen.1007125

Mutations in Caenorhabditis elegans neuroligin-like glit-1, the apoptosis pathway and the calcium chaperone crt-1 increase dopaminergic neurodegeneration after 6-OHDA treatment

Sarah-Lena Offenburger, Elisabeth Jongsma, Anton Gartner

PLOS Genetics: published January 18, 2018 | https://doi.org/10.1371/journal.pgen.1007106

Wor1 establishes opaque cell fate through inhibition of the general co-repressor Tup1 in Candida albicans

Selma S. Alkafeef, Clinton Yu, Lan Huang, Haoping Liu

PLOS Genetics: published January 16, 2018 | https://doi.org/10.1371/journal.pgen.1007176

Differentially-dimensioned furrow formation by zygotic gene expression and the MBT

Yi Xie, J. Todd Blankenship

PLOS Genetics: published January 16, 2018 | https://doi.org/10.1371/journal.pgen.1007174

The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

Khanh Dao Duc, Yun S. Song

PLOS Genetics: published January 16, 2018 | https://doi.org/10.1371/journal.pgen.1007166

Ovule identity mediated by pre-mRNA processing in Arabidopsis

Encarnación Rodríguez-Cazorla, Samanta Ortuño-Miquel, Héctor Candela, Lindsay J. Bailey-Steinitz, Martin F. Yanofsky, Antonio Martínez-Laborda, Juan-José Ripoll, Antonio Vera

PLOS Genetics: published January 12, 2018 | https://doi.org/10.1371/journal.pgen.1007182

MORC2B is essential for meiotic progression and fertility

Baolu Shi, Jiangyang Xue, Jian Zhou, Seth D. Kasowitz, Yuanwei Zhang, Guanxiang Liang, Yongjuan Guan, Qinghua Shi, Mingxi Liu, Jiahao Sha, Xiaoyan Huang, P. Jeremy Wang

PLOS Genetics: published January 12, 2018 | https://doi.org/10.1371/journal.pgen.1007175

Identification of an elaborate NK-specific system regulating HLA-C expression

Hongchuan Li, Martin A. Ivarsson, Victoria E. Walker-Sperling, Jeff Subleski, Jenna K. Johnson, Paul W. Wright, Mary Carrington, Niklas K. Björkström, Daniel W. McVicar, Stephen K. Anderson

PLOS Genetics: published January 12, 2018 | https://doi.org/10.1371/journal.pgen.1007163

Glass promotes the differentiation of neuronal and non-neuronal cell types in the Drosophila eye

Carolyn A. Morrison, Hao Chen, Tiffany Cook, Stuart Brown, Jessica E. Treisman

PLOS Genetics: published January 11, 2018 | https://doi.org/10.1371/journal.pgen.1007173

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

Morgan N. Price, Grant M. Zane, Jennifer V. Kuehl, Ryan A. Melnyk, Judy D. Wall, Adam M. Deutschbauer, Adam P. Arkin

PLOS Genetics: published January 11, 2018 | https://doi.org/10.1371/journal.pgen.1007147

Brassinosteroids regulate root growth by controlling reactive oxygen species homeostasis and dual effect on ethylene synthesis in Arabidopsis

Bingsheng Lv, Huiyu Tian, Feng Zhang, Jiajia Liu, Songchong Lu, Mingyi Bai, Chuanyou Li, Zhaojun Ding

PLOS Genetics: published January 11, 2018 | https://doi.org/10.1371/journal.pgen.1007144

Adipose tissue ATGL modifies the cardiac lipidome in pressure-overload-induced left ventricular failure

Janek Salatzki, Anna Foryst-Ludwig, Kajetan Bentele, Annelie Blumrich, Elia Smeir, Zsofia Ban, Sarah Brix, Jana Grune, Niklas Beyhoff, Robert Klopfleisch, Sebastian Dunst, Michal A. Surma, Christian Klose, Michael Rothe, Frank R. Heinzel, Alexander Krannich, Erin E. Kershaw, Dieter Beule, P. Christian Schulze, Nikolaus Marx, Ulrich Kintscher

PLOS Genetics: published January 10, 2018 | https://doi.org/10.1371/journal.pgen.1007171

Cdc73 suppresses genome instability by mediating telomere homeostasis

Rahul V. Nene, Christopher D. Putnam, Bin-Zhong Li, Katarina G. Nguyen, Anjana Srivatsan, Christopher S. Campbell, Arshad Desai, Richard D. Kolodner

PLOS Genetics: published January 10, 2018 | https://doi.org/10.1371/journal.pgen.1007170

Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival

Arie Zackay, James A. Cotton, Mandy Sanders, Asrat Hailu, Abedelmajeed Nasereddin, Alon Warburg, Charles L. Jaffe

PLOS Genetics: published January 9, 2018 | https://doi.org/10.1371/journal.pgen.1007133

Cover

RNA processing and plant ovule identity.

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