PLOS Genetics - Číslo 10/2020

Perspective

1008997
How noncrossover homologs are conjoined and segregated in Drosophila male meiosis I: Stable but reversible homolog linkers require a novel Separase target protein

Elsie E. Adams, Qiutao He, Bruce D. McKee

1009045
The ninth life of the cat reference genome, Felis_catus

Wengang Zhang, Jeffrey J. Schoenebeck


Correction

1009131
Correction: Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development

Robert L. Baker, Wen Fung Leong, Marcus T. Brock, Matthew J. Rubin, R. J. Cody Markelz, Stephen Welch, Julin N. Maloof, Cynthia Weinig

1009138
Correction: Ferritin heavy chain protects the developing wing from reactive oxygen species and ferroptosis

Simone Mumbauer, Justine Pascual, Irina Kolotuev, Fisun Hamaratoglu

1009139
Correction: Molecular predictors of brain metastasis-related microRNAs in lung adenocarcinoma

Guogui Sun, Xiao Ding, Nan Bi, Zhiwu Wang, Lihong Wu, Wei Zhou, Zitong Zhao, Jingbo Wang, Weimin Zhang, Jing Fan, WenJue Zhang, Xin Dong, Ning Lv, Yongmei Song, Qimin Zhan, LuHua Wang

1009147
Correction: A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage
1009148
Correction: Architecture of the Escherichia coli nucleoid

Subhash C. Verma, Zhong Qian, Sankar L. Adhya

1009151
Correction: The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes

Daniel Andergassen, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski, Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian M. Pauler, Quanah J. Hudson

1009152
Correction: Telomere length-dependent transcription and epigenetic modifications in promoters remote from telomere ends

Ananda Kishore Mukherjee, Shalu Sharma, Suman Sengupta, Dhurjhoti Saha, Pankaj Kumar, Tabish Hussain, Vivek Srivastava, Sumitabho Deb Roy, Jerry W. Shay, Shantanu Chowdhury

1009156
Correction: yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development

Bernardo Blanco-Sánchez, Aurélie Clément, Sarah J. Stednitz, Jennifer Kyle, Judy L. Peirce, Marcie McFadden, Jeremy Wegner, Jennifer B. Phillips, Ellen Macnamara, Yan Huang, David R. Adams, Camilo Toro, William A. Gahl, May Christine V. Malicdan, Cynthia J. Tifft, Erika M. Zink, Kent J. Bloodsworth, Kelly G. Stratton, , David M. Koeller, Thomas O. Metz, Philip Washbourne, Monte Westerfield

1009158
Correction: Leveraging correlations between variants in polygenic risk scores to detect heterogeneity in GWAS cohorts

Jie Yuan, Hengrui Xing, Alexandre Louis Lamy, , Todd Lencz, Itsik Pe’er


Topic Page

1009034
RNA-directed DNA Methylation

Robert M. Erdmann, Colette L. Picard


Research Article

1008623
Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots

Emily E. Wear, Jawon Song, Gregory J. Zynda, Leigh Mickelson-Young, Chantal LeBlanc, Tae-Jin Lee, David O. Deppong, George C. Allen, Robert A. Martienssen, Matthew W. Vaughn, Linda Hanley-Bowdoin, William F. Thompson

1008627
A single Ho-induced double-strand break at the MAT locus is lethal in Candida glabrata

Laetitia Maroc, Youfang Zhou-Li, Stéphanie Boisnard, Cécile Fairhead

1008689
A Rad51-independent pathway promotes single-strand template repair in gene editing

Danielle N. Gallagher, Nhung Pham, Annie M. Tsai, Abigail N. Janto, Jihyun Choi, Grzegorz Ira, James E. Haber

1008718
Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits

Suzanne Vogelezang, Jonathan P. Bradfield, Tarunveer S. Ahluwalia, John A. Curtin, Timo A. Lakka, Niels Grarup, Markus Scholz, Peter J. van der Most, Claire Monnereau, Evie Stergiakouli, Anni Heiskala, Momoko Horikoshi, Iryna O. Fedko, Natalia Vilor-Tejedor, Diana L. Cousminer, Marie Standl, Carol A. Wang, Jorma Viikari, Frank Geller, Carmen Iñiguez, Niina Pitkänen, Alessandra Chesi, Jonas Bacelis, Loic Yengo, Maties Torrent, Ioanna Ntalla, Øyvind Helgeland, Saskia Selzam, Judith M. Vonk, Mohammed H. Zafarmand, Barbara Heude, Ismaa Sadaf Farooqi, Akram Alyass, Robin N. Beaumont, Christian T. Have, Peter Rzehak, Jose Ramon Bilbao, Theresia M. Schnurr, Inês Barroso, Klaus Bønnelykke, Lawrence J. Beilin, Lisbeth Carstensen, Marie-Aline Charles, Bo Chawes, Karine Clément, Ricardo Closa-Monasterolo, Adnan Custovic, Johan G. Eriksson, Joaquin Escribano, Maria Groen-Blokhuis, Veit Grote, Dariusz Gruszfeld, Hakon Hakonarson, Torben Hansen, Andrew T. Hattersley, Mette Hollensted, Jouke-Jan Hottenga, Elina Hyppönen, Stefan Johansson, Raimo Joro, Mika Kähönen, Ville Karhunen, Wieland Kiess, Bridget A. Knight, Berthold Koletzko, Andreas Kühnapfel, Kathrin Landgraf, Jean-Paul Langhendries, Terho Lehtimäki, Jaakko T. Leinonen, Aihuali Li, Virpi Lindi, Estelle Lowry, Mariona Bustamante, Carolina Medina-Gomez, Mads Melbye, Kim F. Michaelsen, Camilla S. Morgen, Trevor A. Mori, Tenna R. H. Nielsen, Harri Niinikoski, Albertine J. Oldehinkel, Katja Pahkala, Kalliope Panoutsopoulou, Oluf Pedersen, Craig E. Pennell, Christine Power, Sijmen A. Reijneveld, Fernando Rivadeneira, Angela Simpson, Peter D. Sly, Jakob Stokholm, Kook K. Teo, Elisabeth Thiering, Nicholas J. Timpson, André G. Uitterlinden, Catharina E. M. van Beijsterveldt, Barbera D. C. van Schaik, Marc Vaudel, Elvira Verduci, Rebecca K. Vinding, Mandy Vogel, Eleftheria Zeggini, Sylvain Sebert, Mads V. Lind, Christopher D. Brown, Loreto Santa-Marina, Eva Reischl, Christine Frithioff-Bøjsøe, David Meyre, Eleanor Wheeler, Ken Ong, Ellen A. Nohr, Tanja G. M. Vrijkotte, Gerard H. Koppelman, Robert Plomin, Pål R. Njølstad, George D. Dedoussis, Philippe Froguel, Thorkild I. A. Sørensen, Bo Jacobsson, Rachel M. Freathy, Babette S. Zemel, Olli Raitakari, Martine Vrijheid, Bjarke Feenstra, Leo-Pekka Lyytikainen, Harold Snieder, Holger Kirsten, Patrick G. Holt, Joachim Heinrich, Elisabeth Widén, Jordi Sunyer, Dorret I. Boomsma, Marjo-Riitta Jarvelin, Antje Körner, George Davey Smith, Jens-Christian Holm, Mustafa Atalay, Clare Murray, Hans Bisgaard, Mark I. McCarthy, , Vincent W. V. Jaddoe, Struan F. A. Grant, Janine F. Felix, John A. Curtin, Timo A. Lakka, Markus Scholz, Peter J. van der Most, Evie Stergiakouli, Anni Heiskala, Momoko Horikoshi, Iryna O. Fedko, Natalia Vilor-Tejedor, Diana L. Cousminer, Marie Standl, Carol A. Wang, Jorma Viikari, Frank Geller, Carmen Iñiguez, Niina Pitkänen, Alessandra Chesi, Jonas Bacelis, Loic Yengo, Maties Torrent, Ioanna Ntalla, Øyvind Helgeland, Saskia Selzam, Judith M. Vonk, Mohammed H. Zafarmand, Barbara Heude, Ismaa Sadaf Farooqi, Akram Alyass, Robin N. Beaumont, Peter Rzehak, Jose Ramon Bilbao, Inês Barroso, Lawrence J. Beilin, Lisbeth Carstensen, Marie-Aline Charles, Karine Clément, Ricardo Closa-Monasterolo, Adnan Custovic, Johan G. Eriksson, Joaquin Escribano, Maria Groen-Blokhuis, Veit Grote, Dariusz Gruszfeld, Andrew T. Hattersley, Jouke-Jan Hottenga, Elina Hyppönen, Stefan Johansson, Raimo Joro, Mika Kähönen, Ville Karhunen, Wieland Kiess, Bridget A. Knight, Berthold Koletzko, Andreas Kühnapfel, Kathrin Landgraf, Jean-Paul Langhendries, Terho Lehtimäki, Jaakko T. Leinonen, Aihuali Li, Virpi Lindi, Estelle Lowry, Mariona Bustamante, Mads Melbye, Kim F. Michaelsen, Camilla S. Morgen, Trevor A. Mori, Tenna R. H. Nielsen, Harri Niinikoski, Albertine J. Oldehinkel, Katja Pahkala, Kalliope Panoutsopoulou, Craig E. Pennell, Christine Power, Sijmen A. Reijneveld, Angela Simpson, Peter D. Sly, Kook K. Teo, Elisabeth Thiering, Nicholas J. Timpson, Catharina E. M. van Beijsterveldt, Barbera D. C. van Schaik, Marc Vaudel, Elvira Verduci, Mandy Vogel, Eleftheria Zeggini, Sylvain Sebert, Mads V. Lind, Christopher D. Brown, Loreto Santa-Marina, Eva Reischl, David Meyre, Eleanor Wheeler, Ken Ong, Ellen A. Nohr, Tanja G. M. Vrijkotte, Gerard H. Koppelman, Robert Plomin, Pål R. Njølstad, George D. Dedoussis, Philippe Froguel, Bo Jacobsson, Rachel M. Freathy, Babette S. Zemel, Olli Raitakari, Martine Vrijheid, Bjarke Feenstra, Leo-Pekka Lyytikainen, Harold Snieder, Holger Kirsten, Patrick G. Holt, Joachim Heinrich, Elisabeth Widén, Jordi Sunyer, Dorret I. Boomsma, Marjo-Riitta Jarvelin, Antje Körner, George Davey Smith, Mustafa Atalay, Clare Murray, Mark I. McCarthy

1008751
C. elegans CLASP/CLS-2 negatively regulates membrane ingression throughout the oocyte cortex and is required for polar body extrusion

Aleesa J. Schlientz, Bruce Bowerman

1008821
The O-GlcNAc transferase OGT is a conserved and essential regulator of the cellular and organismal response to hypertonic stress

Sarel J. Urso, Marcella Comly, John A. Hanover, Todd Lamitina

1008844
Drosophila phosphatidylinositol-4 kinase fwd promotes mitochondrial fission and can suppress Pink1/parkin phenotypes

Ana Terriente-Felix, Emma L. Wilson, Alexander J. Whitworth

1008926
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

Reuben M. Buckley, Brian W. Davis, Wesley A. Brashear, Fabiana H. G. Farias, Kei Kuroki, Tina Graves, LaDeana W. Hillier, Milinn Kremitzki, Gang Li, Rondo P. Middleton, Patrick Minx, Chad Tomlinson, Leslie A. Lyons, William J. Murphy, Wesley C. Warren

1008928
Chromosome separation during Drosophila male meiosis I requires separase-mediated cleavage of the homolog conjunction protein UNO

Joe Weber, Zeynep Kabakci, Soumya Chaurasia, Erich Brunner, Christian F. Lehner

1009009
Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease

Tian-hao Zhang, Lei Dai, John P. Barton, Yushen Du, Yuxiang Tan, Wenwen Pang, Arup K. Chakraborty, James O. Lloyd-Smith, Ren Sun

1009016
Human ABCB1 with an ABCB11-like degenerate nucleotide binding site maintains transport activity by avoiding nucleotide occlusion

Katalin Goda, Yaprak Dönmez-Cakil, Szabolcs Tarapcsák, Gábor Szalóki, Dániel Szöllősi, Zahida Parveen, Dóra Türk, Gergely Szakács, Peter Chiba, Thomas Stockner

1009022
Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation

Brendan Evano, Diljeet Gill, Irene Hernando-Herraez, Glenda Comai, Thomas M. Stubbs, Pierre-Henri Commere, Wolf Reik, Shahragim Tajbakhsh

1009033
Dbp5 associates with RNA-bound Mex67 and Nab2 and its localization at the nuclear pore complex is sufficient for mRNP export and cell viability

Rebecca L. Adams, Susan R. Wente

1009035
The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations

Fredrika Åsenius, Tyler J. Gorrie-Stone, Ama Brew, Yasmin Panchbhaya, Elizabeth Williamson, Leonard C. Schalkwyk, Vardhman K. Rakyan, Michelle L. Holland, Sarah J. Marzi, David J. Williams

1009037
A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices

James A. Watson, Aimee R. Taylor, Elizabeth A. Ashley, Arjen Dondorp, Caroline O. Buckee, Nicholas J. White, Chris C. Holmes

1009038
Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas

Erin Calfee, Marcelo Nicolás Agra, María Alejandra Palacio, Santiago R. Ramírez, Graham Coop, Marcelo Nicolás Agra, María Alejandra Palacio

1009041
Extensive trimming of short single-stranded DNA oligonucleotides during replication-coupled gene editing in mammalian cells

Thomas W. van Ravesteyn, Marcos Arranz Dols, Wietske Pieters, Marleen Dekker, Hein te Riele

1009042
Selection for ancient periodic motifs that do not impart DNA bending

Aletheia Atzinger, Jeffrey G. Lawrence

1009046
The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity

Hongfeng Chen, P. Winston Miller, Daniel L. Johnson, R. Nicholas Laribee

1009052
Mutation of NEKL-4/NEK10 and TTLL genes suppress neuronal ciliary degeneration caused by loss of CCPP-1 deglutamylase function

Kade M. Power, Jyothi S. Akella, Amanda Gu, Jonathon D. Walsh, Sebastian Bellotti, Margaret Morash, Winnie Zhang, Yasmin H. Ramadan, Nicole Ross, Andy Golden, Harold E. Smith, Maureen M. Barr, Robert O’Hagan

1009054
Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases

Elena Díaz-Santiago, Fernando M. Jabato, Elena Rojano, Pedro Seoane, Florencio Pazos, James R. Perkins, Juan A. G. Ranea

1009056
Cells with loss-of-heterozygosity after exposure to ionizing radiation in Drosophila are culled by p53-dependent and p53-independent mechanisms

Jeremy Brown, Inle Bush, Justine Bozon, Tin Tin Su

1009064
Insulin signaling represents a gating mechanism between different memory phases in Drosophila larvae

Melanie Eschment, Hanna R. Franz, Nazlı Güllü, Luis G. Hölscher, Ko-Eun Huh, Annekathrin Widmann

1009065
Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study

Marco Galardini, Olivier Clermont, Alexandra Baron, Bede Busby, Sara Dion, Sören Schubert, Pedro Beltrao, Erick Denamur

1009068
Identification of the transcription factor Miz1 as an essential regulator of diphthamide biosynthesis using a CRISPR-mediated genome-wide screen

Jie Liu, Zehua Zuo, Meijuan Zou, Toren Finkel, Shihui Liu

1009069
Mesenchyme-derived IGF2 is a major paracrine regulator of pancreatic growth and function

Constanze M. Hammerle, Ionel Sandovici, Gemma V. Brierley, Nicola M. Smith, Warren E. Zimmer, Ilona Zvetkova, Haydn M. Prosser, Yoichi Sekita, Brian Y. H. Lam, Marcella Ma, Wendy N. Cooper, Antonio Vidal-Puig, Susan E. Ozanne, Gema Medina-Gómez, Miguel Constância

1009070
PE homeostasis rebalanced through mitochondria-ER lipid exchange prevents retinal degeneration in Drosophila

Haifang Zhao, Tao Wang

1009076
Chromosome number evolves at equal rates in holocentric and monocentric clades

Sarah N. Ruckman, Michelle M. Jonika, Claudio Casola, Heath Blackmon

1009078
Genetically predicted telomere length is associated with clonal somatic copy number alterations in peripheral leukocytes

Derek W. Brown, Shu-Hong Lin, Po-Ru Loh, Stephen J. Chanock, Sharon A. Savage, Mitchell J. Machiela

1009081
Metabolism of long-chain fatty acids affects disulfide bond formation in Escherichia coli and activates envelope stress response pathways as a combat strategy

Kanchan Jaswal, Megha Shrivastava, Deeptodeep Roy, Shashank Agrawal, Rachna Chaba

1009082
Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

Yann Bourgeois, Robert Ruggiero, Imtiyaz Hariyani, Stéphane Boissinot, Robert P. Ruggiero, Imtiyaz Hariyani, Stéphane Boissinot

1009085
DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines

Alexandre Duprey, Eduardo A. Groisman

1009087
Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing

Kashyap Chhatbar, Justyna Cholewa-Waclaw, Ruth Shah, Adrian Bird, Guido Sanguinetti

1009089
Automated feature extraction from population wearable device data identified novel loci associated with sleep and circadian rhythms

Xinyue Li, Hongyu Zhao

1009091
Exploring the Complexity of Protein-Level Dosage Compensation that Fine-Tunes Stoichiometry of Multiprotein Complexes

Koji Ishikawa, Akari Ishihara, Hisao Moriya

1009097
Diversified regulation of circadian clock gene expression following whole genome duplication

Alexander C. West, Marianne Iversen, Even H. Jørgensen, Simen R. Sandve, David G. Hazlerigg, Shona H. Wood

1009098
Loss of the RNA trimethylguanosine cap is compatible with nuclear accumulation of spliceosomal snRNAs but not pre-mRNA splicing or snRNA processing during animal development

Lin Cheng, Yu Zhang, Yi Zhang, Tao Chen, Yong-Zhen Xu, Yikang S. Rong

1009100
Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies

Anya T. Joynt, Taylor A. Evans, Matthew J. Pellicore, Emily F. Davis-Marcisak, Melis A. Aksit, Alice C. Eastman, Shivani U. Patel, Kathleen C. Paul, Derek L. Osorio, Alyssa D. Bowling, Calvin U. Cotton, Karen S. Raraigh, Natalie E. West, Christian A. Merlo, Garry R. Cutting, Neeraj Sharma

1009102
Tissue-specific isoforms of the single C. elegans Ryanodine receptor gene unc-68 control specific functions

Filipe Marques, Saurabh Thapliyal, Avelino Javer, Priyanka Shrestha, André E. X. Brown, Dominique A. Glauser

1009103
A high-throughput CRISPR interference screen for dissecting functional regulators of GPCR/cAMP signaling

Khairunnisa Mentari Semesta, Ruilin Tian, Martin Kampmann, Mark von Zastrow, Nikoleta G. Tsvetanova

1009115
CenH3 distribution reveals extended centromeres in the model beetle Tribolium castaneum

Tena Gržan, Evelin Despot-Slade, Nevenka Meštrović, Miroslav Plohl, Brankica Mravinac

1009118
Inactivation of the mitochondrial protease Afg3l2 results in severely diminished respiratory chain activity and widespread defects in mitochondrial gene expression

Gautam Pareek, Leo J. Pallanck

1009125
Effect of H2A.Z deletion is rescued by compensatory mutations in Fusarium graminearum

Zhenhui Chen, Enric Zehraoui, Anna K. Atanasoff-Kardjalieff, Joseph Strauss, Lena Studt, Nadia Ponts

1009140
Drosophila Caliban preserves intestinal homeostasis and lifespan through regulating mitochondrial dynamics and redox state in enterocytes

Zhaoxia Dai, Dong Li, Xiao Du, Ying Ge, Deborah A. Hursh, Xiaolin Bi

1009141
A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank

Junyang Qian, Yosuke Tanigawa, Wenfei Du, Matthew Aguirre, Chris Chang, Robert Tibshirani, Manuel A. Rivas, Trevor Hastie

1009155
Evolution of linkage and genome expansion in protocells: The origin of chromosomes

András Szilágyi, Viktor Péter Kovács, Eörs Szathmáry, Mauro Santos

1009165
Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for “polygenic epistasis”

Christoph D. Rau, Natalia M. Gonzales, Joshua S. Bloom, Danny Park, Julien Ayroles, Abraham A. Palmer, Aldons J. Lusis, Noah Zaitlen

1009171
DOT-1.1-dependent H3K79 methylation promotes normal meiotic progression and meiotic checkpoint function in C. elegans

Laura I. Lascarez-Lagunas, Esther Herruzo, Alla Grishok, Pedro A. San-Segundo, Mónica P. Colaiácovo

1009173
Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change

Jacob M. Daane, Juliette Auvinet, Alicia Stoebenau, Donald Yergeau, Matthew P. Harris, H. William Detrich, III

1009181
AKH-FOXO pathway regulates starvation-induced sleep loss through remodeling of the small ventral lateral neuron dorsal projections

Qiankun He, Juan Du, Liya Wei, Zhangwu Zhao

1009199
Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling

Christian Lundtoft, Pascal Pucholt, Juliana Imgenberg-Kreuz, Jonas Carlsson-Almlöf, Maija-Leena Eloranta, Ann-Christine Syvänen, Gunnel Nordmark, Johanna K. Sandling, Ingrid Kockum, Tomas Olsson, Lars Rönnblom, Niklas Hagberg


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