April 2019

In Greek mythology, the chimera combined the physical characteristics of several different creatures to make a wholly new beast with attributes both like and unlike its parents. In two independent adaptive laboratory evolution experiments, a recombination event between two maltose sugar transporter genes from the yeast Saccharomyces eubayanus resulted in a chimeric transporter that gained the ability to carry larger maltotriose sugar molecules. The uptake of maltotriose by S. eubayanus is a critical step in being able to ferment a sugar whose consumption is important for the production of high-quality beer. See Baker, Hittinger.

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Image Credit: Graphic created by Emily Baker. The image of the chimera has been released into the public domain by its creator, Pearson Scott Foresman.

Perspective

Genes influence facial attractiveness through intricate biological relationships

Julie D. White, David A. Puts

PLOS Genetics: published April 4, 2019 | https://doi.org/10.1371/journal.pgen.1008030

Reviews

What is mutation? A chapter in the series: How microbes “jeopardize” the modern synthesis

Devon M. Fitzgerald, Susan M. Rosenberg

PLOS Genetics: published April 1, 2019 | https://doi.org/10.1371/journal.pgen.1007995

On the utilization of polygenic risk scores for therapeutic targeting

Greg Gibson

PLOS Genetics: published April 25, 2019 | https://doi.org/10.1371/journal.pgen.1008060

Research Articles

Quantitative mapping of DNA phosphorothioatome reveals phosphorothioate heterogeneity of low modification frequency

Jinli Li, Yi Chen, Tao Zheng, Lingxin Kong, Sucheng Zhu, Yihua Sun, Zixin Deng, Litao Yang, Delin You

PLOS Genetics: published April 1, 2019 | https://doi.org/10.1371/journal.pgen.1008026

Zebrafish Klf4 maintains the ionocyte progenitor population by regulating epidermal stem cell proliferation and lateral inhibition

Yi-Chung Chen, Bo-Kai Liao, Yu-Fen Lu, Yu-Hsiu Liu, Fang-Chi Hsieh, Pung-Pung Hwang, Sheng-Ping L. Hwang

PLOS Genetics: published April 1, 2019 | https://doi.org/10.1371/journal.pgen.1008058

Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function

EmilyClare P. Baker, Chris Todd Hittinger

PLOS Genetics: published April 4, 2019 | https://doi.org/10.1371/journal.pgen.1007786

In vivo recombination of Saccharomyces eubayanus maltose-transporter genes yields a chimeric transporter that enables maltotriose fermentation

Nick Brouwers, Arthur R. Gorter de Vries, Marcel van den Broek, Susan M. Weening, Tom D. Elink Schuurman, Niels G. A. Kuijpers, Jack T. Pronk, Jean-Marc G. Daran

PLOS Genetics: published April 4, 2019 | https://doi.org/10.1371/journal.pgen.1007853

Genome-wide association study reveals sex-specific genetic architecture of facial attractiveness

Bowen Hu, Ning Shen, James J. Li, Hyunseung Kang, Jinkuk Hong, Jason Fletcher, Jan Greenberg, Marsha R. Mailick, Qiongshi Lu

PLOS Genetics: published April 4, 2019 | https://doi.org/10.1371/journal.pgen.1007973

Genome-wide association study in Turkish and Iranian populations identify rare familial Mediterranean fever gene (MEFV) polymorphisms associated with ankylosing spondylitis

Zhixiu Li, Servet Akar, Handan Yarkan, Sau Kuen Lee, Pınar Çetin, Gerçek Can, Gökce Kenar, Fernur Çapa, Omer Nuri Pamuk, Yavuz Pehlivan, Katie Cremin, Erika De Guzman, Jessica Harris, Lawrie Wheeler, Ahmadreza Jamshidi, Mahdi Vojdanian, Elham Farhadi, Nooshin Ahmadzadeh, Zeynep Yüce, Ediz Dalkılıç, Dilek Solmaz, Berrin Akın, Salim Dönmez, İsmail Sarı, Paul J. Leo, Tony J. Kenna, Fatos Önen, Mahdi Mahmoudi, Matthew A. Brown, Nurullah Akkoc

PLOS Genetics: published April 4, 2019 | https://doi.org/10.1371/journal.pgen.1008038

Floral regulators FLC and SOC1 directly regulate expression of the B3-type transcription factor TARGET OF FLC AND SVP 1 at the Arabidopsis shoot apex via antagonistic chromatin modifications

René Richter, Atsuko Kinoshita, Coral Vincent, Rafael Martinez-Gallegos, He Gao, Annabel D. van Driel, Youbong Hyun, Julieta L. Mateos, George Coupland

PLOS Genetics: published April 4, 2019 | https://doi.org/10.1371/journal.pgen.1008065

DSB structure impacts DNA recombination leading to class switching and chromosomal translocations in human B cells

Clare C. So, Alberto Martin

PLOS Genetics: published April 4, 2019 | https://doi.org/10.1371/journal.pgen.1008101

Reverse GWAS: Using genetics to identify and model phenotypic subtypes

Andy Dahl, Na Cai, Arthur Ko, Markku Laakso, Päivi Pajukanta, Jonathan Flint, Noah Zaitlen

PLOS Genetics: published April 5, 2019 | https://doi.org/10.1371/journal.pgen.1008009

Temporal and spatial regulation of protein cross-linking by the pre-assembled substrates of a Bacillus subtilis spore coat transglutaminase

Catarina G. Fernandes, Diogo Martins, Guillem Hernandez, Ana L. Sousa, Carolina Freitas, Erin M. Tranfield, Tiago N. Cordeiro, Mónica Serrano, Charles. P. Moran Jr., Adriano O. Henriques

PLOS Genetics: published April 8, 2019 | https://doi.org/10.1371/journal.pgen.1007912

Loss of atrx cooperates with p53-deficiency to promote the development of sarcomas and other malignancies

Felix Oppel, Ting Tao, Hui Shi, Kenneth N. Ross, Mark W. Zimmerman, Shuning He, Guangxiang Tong, Jon C. Aster, A. Thomas Look

PLOS Genetics: published April 10, 2019 | https://doi.org/10.1371/journal.pgen.1008039

Precise staging of beetle horn formation in Trypoxylus dichotomus reveals the pleiotropic roles of doublesex depending on the spatiotemporal developmental contexts

Shinichi Morita, Toshiya Ando, Akiteru Maeno, Takeshi Mizutani, Mutsuki Mase, Shuji Shigenobu, Teruyuki Niimi

PLOS Genetics: published April 10, 2019 | https://doi.org/10.1371/journal.pgen.1008063

The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis

Xiaolei Wang, Jiong Gao, Shan Gao, Yi Song, Zhen Yang, Benke Kuai

PLOS Genetics: published April 10, 2019 | https://doi.org/10.1371/journal.pgen.1008068

Novel AU-rich proximal UTR sequences (APS) enhance CXCL8 synthesis upon the induction of rpS6 phosphorylation

Zhiwei Ang, Ricky Abdi Gunawan Koean, Jun Zhi Er, Li Ting Lee, John Kit Chung Tam, Huili Guo, Jeak Ling Ding

PLOS Genetics: published April 10, 2019 | https://doi.org/10.1371/journal.pgen.1008077

An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape

Victoria O. Pokusaeva, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen S. Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, Dmitry N. Ivankov, Arseniy V. Akopyan, Sergey Ya. Avvakumov, Inna S. Povolotskaya, Guillaume J. Filion, Lucas B. Carey, Fyodor A. Kondrashov

PLOS Genetics: published April 10, 2019 | https://doi.org/10.1371/journal.pgen.1008079

Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals

Boxun Zhao, Qixi Wu, Adam Yongxin Ye, Jing Guo, Xianing Zheng, Xiaoxu Yang, Linlin Yan, Qing-Rong Liu, Thomas M. Hyde, Liping Wei, August Yue Huang

PLOS Genetics: published April 11, 2019 | https://doi.org/10.1371/journal.pgen.1008043

FOXO3 directly regulates an autophagy network to functionally regulate proteostasis in adult neural stem cells

Amanda J. Audesse, Shleshma Dhakal, Lexi-Amber Hassell, Zachary Gardell, Yuliya Nemtsova, Ashley E. Webb

PLOS Genetics: published April 11, 2019 | https://doi.org/10.1371/journal.pgen.1008097

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

Kelly L. Wyres, Ryan R. Wick, Louise M. Judd, Roni Froumine, Alex Tokolyi, Claire L. Gorrie, Margaret M. C. Lam, Sebastián Duchêne, Adam Jenney, Kathryn E. Holt

PLOS Genetics: published April 15, 2019 | https://doi.org/10.1371/journal.pgen.1008114

Associations of variants In the hexokinase 1 and interleukin 18 receptor regions with oxyhemoglobin saturation during sleep

Brian E. Cade, Han Chen, Adrienne M. Stilp, Tin Louie, Sonia Ancoli-Israel, Raanan Arens, Richard Barfield, Jennifer E. Below, Jianwen Cai, Matthew P. Conomos, Daniel S. Evans, Alexis C. Frazier-Wood, Sina A. Gharib, Kevin J. Gleason, Daniel J. Gottlieb, David R. Hillman, W. Craig Johnson, David J. Lederer, Jiwon Lee, Jose S. Loredo, Hao Mei, Sutapa Mukherjee, Sanjay R. Patel, Wendy S. Post, Shaun M. Purcell, Alberto R. Ramos, Kathryn J. Reid, Ken Rice, Neomi A. Shah, Tamar Sofer, Kent D. Taylor, Timothy A. Thornton, Heming Wang, Kristine Yaffe, Phyllis C. Zee, Craig L. Hanis, Lyle J. Palmer, Jerome I. Rotter, Katie L. Stone, Gregory J. Tranah, James G. Wilson, Shamil R. Sunyaev, Cathy C. Laurie, Xiaofeng Zhu, Richa Saxena, Xihong Lin, Susan Redline

PLOS Genetics: published April 16, 2019 | https://doi.org/10.1371/journal.pgen.1007739

Schwann cells ER-associated degradation contributes to myelin maintenance in adult nerves and limits demyelination in CMT1B mice

Vera G. Volpi, Cinzia Ferri, Ilaria Fregno, Ubaldo Del Carro, Francesca Bianchi, Cristina Scapin, Emanuela Pettinato, Tatiana Solda, M. Laura Feltri, Maurizio Molinari, Lawrence Wrabetz, Maurizio D’Antonio

PLOS Genetics: published April 17, 2019 | https://doi.org/10.1371/journal.pgen.1008069

A stress-response-related inter-compartmental signalling pathway regulates embryonic cuticle integrity in Arabidopsis

Audrey Creff, Lysiane Brocard, Jérôme Joubès, Ludivine Taconnat, Nicolas M. Doll, Anne-Charlotte Marsollier, Stéphanie Pascal, Roberta Galletti, Sophy Boeuf, Steven Moussu, Thomas Widiez, Frédéric Domergue, Gwyneth Ingram

PLOS Genetics: published April 18, 2019 | https://doi.org/10.1371/journal.pgen.1007847

Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage

Chihiro Horigome, Eri Unozawa, Takamasa Ooki, Takehiko Kobayashi

PLOS Genetics: published April 18, 2019 | https://doi.org/10.1371/journal.pgen.1008103

Varicose veins of lower extremities: Insights from the first large-scale genetic study

Alexandra S. Shadrina, Sodbo Z. Sharapov, Tatiana I. Shashkova, Yakov A. Tsepilov

PLOS Genetics: published April 18, 2019 | https://doi.org/10.1371/journal.pgen.1008110

Discovery and characterization of variance QTLs in human induced pluripotent stem cells

Abhishek K. Sarkar, Po-Yuan Tung, John D. Blischak, Jonathan E. Burnett, Yang I. Li, Matthew Stephens, Yoav Gilad

PLOS Genetics: published April 19, 2019 | https://doi.org/10.1371/journal.pgen.1008045

The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana

Elodie Marchadier, Mathieu Hanemian, Sébastien Tisné, Liên Bach, Christos Bazakos, Elodie Gilbault, Parham Haddadi, Laetitia Virlouvet, Olivier Loudet

PLOS Genetics: published April 22, 2019 | https://doi.org/10.1371/journal.pgen.1007954

A small RNA controls bacterial sensitivity to gentamicin during iron starvation

Sylvia Chareyre, Frédéric Barras, Pierre Mandin

PLOS Genetics: published April 22, 2019 | https://doi.org/10.1371/journal.pgen.1008078

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline

Vitor R. C. Aguiar, Jônatas César, Olivier Delaneau, Emmanouil T. Dermitzakis, Diogo Meyer

PLOS Genetics: published April 22, 2019 | https://doi.org/10.1371/journal.pgen.1008091

Destabilization of chromosome structure by histone H3 lysine 27 methylation

Mareike Möller, Klaas Schotanus, Jessica L. Soyer, Janine Haueisen, Kathrin Happ, Maja Stralucke, Petra Happel, Kristina M. Smith, Lanelle R. Connolly, Michael Freitag, Eva H. Stukenbrock

PLOS Genetics: published April 22, 2019 | https://doi.org/10.1371/journal.pgen.1008093

Osmolyte accumulation regulates the SUMOylation and inclusion dynamics of the prionogenic Cyc8-Tup1 transcription corepressor

Cory M. Nadel, Timothy D. Mackie, Richard G. Gardner

PLOS Genetics: published April 22, 2019 | https://doi.org/10.1371/journal.pgen.1008115

CD34 defines melanocyte stem cell subpopulations with distinct regenerative properties

Sandeep S. Joshi, Bishal Tandukar, Li Pan, Jennifer M. Huang, Ferenc Livak, Barbara J. Smith, Theresa Hodges, Anup A. Mahurkar, Thomas J. Hornyak

PLOS Genetics: published April 24, 2019 | https://doi.org/10.1371/journal.pgen.1008034

The Noonan Syndrome-linked Raf1^L613V mutation drives increased glial number in the mouse cortex and enhanced learning

Michael C. Holter, Lauren. T. Hewitt, Stephanie V. Koebele, Jessica M. Judd, Lei Xing, Heather A. Bimonte-Nelson, Cheryl D. Conrad, Toshiyuki Araki, Benjamin G. Neel, William D. Snider, Jason M. Newbern

PLOS Genetics: published April 24, 2019 | https://doi.org/10.1371/journal.pgen.1008108

Infection mechanisms and putative effector repertoire of the mosquito pathogenic oomycete Pythium guiyangense uncovered by genomic analysis

Danyu Shen, Zhaoyang Tang, Cong Wang, Jing Wang, Yumei Dong, Yang Chen, Yun Wei, Biao Cheng, Meiqian Zhang, Laura J. Grenville-Briggs, Brett M. Tyler, Daolong Dou, Ai Xia

PLOS Genetics: published April 24, 2019 | https://doi.org/10.1371/journal.pgen.1008116

Anteroposterior patterning of the zebrafish ear through Fgf- and Hh-dependent regulation of hmx3a expression

Ryan D. Hartwell, Samantha J. England, Nicholas A. M. Monk, Nicholas J. van Hateren, Sarah Baxendale, Mar Marzo, Katharine E. Lewis, Tanya T. Whitfield

PLOS Genetics: published April 25, 2019 | https://doi.org/10.1371/journal.pgen.1008051

Genetic dissection of Escherichia coli's master diguanylate cyclase DgcE: Role of the N-terminal MASE1 domain and direct signal input from a GTPase partner system

Vanessa Pfiffer, Olga Sarenko, Alexandra Possling, Regine Hengge

PLOS Genetics: published April 25, 2019 | https://doi.org/10.1371/journal.pgen.1008059

Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians

Julio E. Molineros, Loren L. Looger, Kwangwoo Kim, Yukinori Okada, Chikashi Terao, Celi Sun, Xu-jie Zhou, Prithvi Raj, Yuta Kochi, Akari Suzuki, Shuji Akizuki, Shuichiro Nakabo, So-Young Bang, Hye-Soon Lee, Young Mo Kang, Chang-Hee Suh, Won Tae Chung, Yong-Beom Park, Jung-Yoon Choe, Seung-Cheol Shim, Shin-Seok Lee, Xiaoxia Zuo, Kazuhiko Yamamoto, Quan-Zhen Li, Nan Shen, Lauren L. Porter, John B. Harley, Kek Heng Chua, Hong Zhang, Edward K. Wakeland, Betty P. Tsao, Sang-Cheol Bae, Swapan K. Nath

PLOS Genetics: published April 25, 2019 | https://doi.org/10.1371/journal.pgen.1008092

Selective advantages favour high genomic AT-contents in intracellular elements

Anne-Kathrin Dietel, Holger Merker, Martin Kaltenpoth, Christian Kost

PLOS Genetics: published April 29, 2019 | https://doi.org/10.1371/journal.pgen.1007778

Genetics of adaptation in modern chicken

Saber Qanbari, Carl-Johan Rubin, Khurram Maqbool, Steffen Weigend, Annett Weigend, Johannes Geibel, Susanne Kerje, Christine Wurmser, Andrew Townsend Peterson, I. Lehr Brisbin Jr., Ruedi Preisinger, Ruedi Fries, Henner Simianer, Leif Andersson

PLOS Genetics: published April 29, 2019 | https://doi.org/10.1371/journal.pgen.1007989

FunSPU: A versatile and adaptive multiple functional annotation-based association test of whole-genome sequencing data

Yiding Ma, Peng Wei

PLOS Genetics: published April 29, 2019 | https://doi.org/10.1371/journal.pgen.1008081

Mutations in PIK3C2A cause syndromic short stature, skeletal abnormalities, and cataracts associated with ciliary dysfunction

Dov Tiosano, Hagit N. Baris, Anlu Chen, Marrit M. Hitzert, Markus Schueler, Federico Gulluni, Antje Wiesener, Antonio Bergua, Adi Mory, Brett Copeland, Joseph G. Gleeson, Patrick Rump, Hester van Meer, Deborah A. Sival, Volker Haucke, Josh Kriwinsky, Karl X. Knaup, André Reis, Nadine N. Hauer, Emilio Hirsch, Ronald Roepman, Rolph Pfundt, Christian T. Thiel, Michael S. Wiesener, Mariam G. Aslanyan, David A. Buchner

PLOS Genetics: published April 29, 2019 | https://doi.org/10.1371/journal.pgen.1008088