Transposable element landscapes in aging Drosophila

Nachen Yang, Satyam P. Srivastav, Reazur Rahman, Qicheng Ma, Gargi Dayama, Sizheng Li, Madoka Chinen, Elissa P. Lei, Michael Rosbash, Nelson C. Lau

PLOS Genetics: published March 3, 2022 | https://doi.org/10.1371/journal.pgen.1010024

Proteome-wide Mendelian randomization identifies causal links between blood proteins and severe COVID-19

Alish B. Palmos, Vincent Millischer, David K. Menon, Timothy R. Nicholson, Leonie S. Taams, Benedict Michael, Geraint Sunderland, Michael J. Griffiths, COVID Clinical Neuroscience Study Consortium, Christopher Hübel, Gerome Breen

PLOS Genetics: published March 3, 2022 | https://doi.org/10.1371/journal.pgen.1010042

ER-PM membrane contact site regulation by yeast ORPs and membrane stress pathways

Evan Quon, Aleksa Nenadic, Mohammad F. Zaman, Jesper Johansen, Christopher T. Beh

PLOS Genetics: published March 3, 2022 | https://doi.org/10.1371/journal.pgen.1010106

Co-transmission of neuropeptides and monoamines choreograph the C. elegans escape response

Jeremy T. Florman, Mark J. Alkema

PLOS Genetics: published March 3, 2022 | https://doi.org/10.1371/journal.pgen.1010091

CTP sensing and Mec1^ATR-Rad53^CHK1/CHK2 mediate a two-layered response to inhibition of glutamine metabolism

Arta Ajazi, Ramveer Choudhary, Laura Tronci, Angela Bachi, Christopher Bruhn

PLOS Genetics: published March 3, 2022 | https://doi.org/10.1371/journal.pgen.1010101

PIN3 positively regulates the late initiation of ovule primordia in Arabidopsis thaliana

Li-Qin Hu, Jin-Hui Chang, Shi-Xia Yu, Yu-Tong Jiang, Rong-Han Li, Ji-Xuan Zheng, Yan-Jie Zhang, Hong-Wei Xue, Wen-Hui Lin

PLOS Genetics: published March 4, 2022 | https://doi.org/10.1371/journal.pgen.1010077

Gut-derived peptidoglycan remotely inhibits bacteria dependent activation of SREBP by Drosophila adipocytes

Bernard Charroux, Julien Royet

PLOS Genetics: published March 4, 2022 | https://doi.org/10.1371/journal.pgen.1010098

Comparative therapeutic strategies for preventing aortic rupture in a mouse model of vascular Ehlers-Danlos syndrome

Anne Legrand, Charline Guery, Julie Faugeroux, Erika Fontaine, Carole Beugnon, Amélie Gianfermi, Irmine Loisel-Ferreira, Marie-Christine Verpont, Salma Adham, Tristan Mirault, Juliette Hadchouel, Xavier Jeunemaitre

PLOS Genetics: published March 4, 2022 | https://doi.org/10.1371/journal.pgen.1010059

Rod genesis driven by mafba in an nrl knockout zebrafish model with altered photoreceptor composition and progressive retinal degeneration

Fei Liu, Yayun Qin, Yuwen Huang, Pan Gao, Jingzhen Li, Shanshan Yu, Danna Jia, Xiang Chen, Yuexia Lv, Jiayi Tu, Kui Sun, Yunqiao Han, James Reilly, Xinhua Shu, Qunwei Lu, Zhaohui Tang, Chengqi Xu, Daji Luo, Mugen Liu

PLOS Genetics: published March 4, 2022 | https://doi.org/10.1371/journal.pgen.1009841

Differential synthesis of novel small protein times Salmonella virulence program

Hubert Salvail, Jeongjoon Choi, Eduardo A. Groisman

PLOS Genetics: published March 4, 2022 | https://doi.org/10.1371/journal.pgen.1010074

The VIL gene CRAWLING ELEPHANT controls maturation and differentiation in tomato via polycomb silencing

Ido Shwartz, Chen Yahav, Neta Kovetz, Matan Levy, Alon Israeli, Maya Bar, Katherine L. Duval, Ellen G. Krall, Naama Teboul, José M. Jiménez-Gómez, Roger B. Deal, Naomi Ori

PLOS Genetics: published March 7, 2022 | https://doi.org/10.1371/journal.pgen.1009633

Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources

Andrea Cillingová, Renáta Tóth, Anna Mojáková, Igor Zeman, Romana Vrzoňová, Barbara Siváková, Peter Baráth, Martina Neboháčová, Zuzana Klepcová, Filip Brázdovič, Hana Lichancová, Viktória Hodorová, Broňa Brejová, Tomáš Vinař, Sofia Mutalová, Veronika Vozáriková, Giacomo Mutti, Ľubomír Tomáška, Atilla Gácser, Toni Gabaldón, Jozef Nosek

PLOS Genetics: published March 7, 2022 | https://doi.org/10.1371/journal.pgen.1009815

Set2 histone methyltransferase regulates transcription coupled-nucleotide excision repair in yeast

Kathiresan Selvam, Dalton A. Plummer, Peng Mao, John J. Wyrick

PLOS Genetics: published March 9, 2022 | https://doi.org/10.1371/journal.pgen.1010085

The nitrate-inducible NAC transcription factor NAC056 controls nitrate assimilation and promotes lateral root growth in Arabidopsis thaliana

Peipei Xu, Wei Ma, Jinbo Hu, Weiming Cai

PLOS Genetics: published March 9, 2022 | https://doi.org/10.1371/journal.pgen.1010090

Evolutionary insights into primate skeletal gene regulation using a comparative cell culture model

Genevieve Housman, Emilie Briscoe, Yoav Gilad

PLOS Genetics: published March 9, 2022 | https://doi.org/10.1371/journal.pgen.1010073

Congenital idiopathic megaesophagus in the German shepherd dog is a sex-differentiated trait and is associated with an intronic variable number tandem repeat in Melanin-Concentrating Hormone Receptor 2

Sarah M. Bell, Jacquelyn M. Evans, Katy M. Evans, Kate L. Tsai, Rooksana E. Noorai, Thomas R. Famula, Dolores M. Holle, Leigh Anne Clark

PLOS Genetics: published March 10, 2022 | https://doi.org/10.1371/journal.pgen.1010044

mTOR activity is essential for retinal pigment epithelium regeneration in zebrafish

Fangfang Lu, Lyndsay L. Leach, Jeffrey M. Gross

PLOS Genetics: published March 10, 2022 | https://doi.org/10.1371/journal.pgen.1009628

Box C/D small nucleolar ribonucleoproteins regulate mitochondrial surveillance and innate immunity

Elissa Tjahjono, Alexey V. Revtovich, Natalia V. Kirienko

PLOS Genetics: published March 11, 2022 | https://doi.org/10.1371/journal.pgen.1010103

Identification of an evolutionarily conserved domain in Neurod1 favouring enteroendocrine versus goblet cell fate

Anne Sophie Reuter, David Stern, Alice Bernard, Chiara Goossens, Arnaud Lavergne, Lydie Flasse, Virginie Von Berg, Isabelle Manfroid, Bernard Peers, Marianne L. Voz

PLOS Genetics: published March 14, 2022 | https://doi.org/10.1371/journal.pgen.1010109

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities

Lajos Kalmar, Srishti Gupta, Iain R. L. Kean, Xiaoliang Ba, Nazreen Hadjirin, Elizabeth M. Lay, Stefan P. W. de Vries, Michael Bateman, Harriet Bartlet, Juan Hernandez-Garcia, Alexander W. Tucker, Olivier Restif, Mark P. Stevens, James L. N. Wood, Duncan J. Maskell, Andrew J. Grant, Mark A. Holmes

PLOS Genetics: published March 14, 2022 | https://doi.org/10.1371/journal.pgen.1009776

eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects

Vasyl Zhabotynsky, Licai Huang, Paul Little, Yi-Juan Hu, Fernando Pardo-Manuel de Villena, Fei Zou, Wei Sun

PLOS Genetics: published March 14, 2022 | https://doi.org/10.1371/journal.pgen.1010076

A shared ancient enhancer element differentially regulates the bric-a-brac tandem gene duplicates in the developing Drosophila leg

Henri-Marc G. Bourbon, Mikhail H. Benetah, Emmanuelle Guillou, Luis Humberto Mojica-Vazquez, Aissette Baanannou, Sandra Bernat-Fabre, Vincent Loubiere, Frédéric Bantignies, Giacomo Cavalli, Muriel Boube

PLOS Genetics: published March 16, 2022 | https://doi.org/10.1371/journal.pgen.1010083

Cytosolic O-GlcNAcylation and PNG1 maintain Drosophila gut homeostasis by regulating proliferation and apoptosis

Hyun-jin Na, Lara K. Abramowitz, John A. Hanover

PLOS Genetics: published March 16, 2022 | https://doi.org/10.1371/journal.pgen.1010128

Biallelic variants in TRAPPC10 cause a microcephalic TRAPPopathy disorder in humans and mice

Lettie E. Rawlins, Hashem Almousa, Shazia Khan, Stephan C. Collins, Miroslav P. Milev, Joseph Leslie, Djenann Saint-Dic, Valeed Khan, Ana Maria Hincapie, Jacob O. Day, Lucy McGavin, Christine Rowley, Gaurav V. Harlalka, Valerie E. Vancollie, Wasim Ahmad, Christopher J. Lelliott, Asma Gul, Binnaz Yalcin, Andrew H. Crosby, Michael Sacher, Emma L. Baple

PLOS Genetics: published March 17, 2022 | https://doi.org/10.1371/journal.pgen.1010114

Impact of nonrandom selection mechanisms on the causal effect estimation for two-sample Mendelian randomization methods

Yuanyuan Yu, Lei Hou, Xu Shi, Xiaoru Sun, Xinhui Liu, Yifan Yu, Zhongshang Yuan, Hongkai Li, Fuzhong Xue

PLOS Genetics: published March 17, 2022 | https://doi.org/10.1371/journal.pgen.1010107

BmPMFBP1 regulates the development of eupyrene sperm in the silkworm, Bombyx mori

Dehong Yang, Jun Xu, Kai Chen, Yujia Liu, Xu Yang, Linmeng Tang, Xingyu Luo, Zulian Liu, Muwang Li, James R. Walters, Yongping Huang

PLOS Genetics: published March 21, 2022 | https://doi.org/10.1371/journal.pgen.1010131

HiCuT: An efficient and low input method to identify protein-directed chromatin interactions

Satish Sati, Parker Jones, Hali S. Kim, Linda A. Zhou, Emmanuel Rapp-Reyes, Thomas H. Leung

PLOS Genetics: published March 23, 2022 | https://doi.org/10.1371/journal.pgen.1010121

Meiotic, genomic and evolutionary properties of crossover distribution in Drosophila yakuba

Nikale Pettie, Ana Llopart, Josep M. Comeron

PLOS Genetics: published March 23, 2022 | https://doi.org/10.1371/journal.pgen.1010087

Significant sparse polygenic risk scores across 813 traits in UK Biobank

Yosuke Tanigawa, Junyang Qian, Guhan Venkataraman, Johanne Marie Justesen, Ruilin Li, Robert Tibshirani, Trevor Hastie, Manuel A. Rivas

PLOS Genetics: published March 24, 2022 | https://doi.org/10.1371/journal.pgen.1010105

Genome wide association study of Escherichia coli bloodstream infection isolates identifies genetic determinants for the portal of entry but not fatal outcome

Erick Denamur, Bénédicte Condamine, Marina Esposito-Farèse, Guilhem Royer, Olivier Clermont, Cédric Laouenan, Agnès Lefort, Victoire de Lastours, Marco Galardini, the COLIBAFI, SEPTICOLI groups

PLOS Genetics: published March 24, 2022 | https://doi.org/10.1371/journal.pgen.1010112

Stonewall prevents expression of ectopic genes in the ovary and accumulates at insulator elements in D. melanogaster

Daniel Zinshteyn, Daniel A. Barbash

PLOS Genetics: published March 24, 2022 | https://doi.org/10.1371/journal.pgen.1010110

SUMO-mediated recruitment allows timely function of the Yen1 nuclease in mitotic cells

Hugo Dorison, Ibtissam Talhaoui, Gerard Mazón

PLOS Genetics: published March 25, 2022 | https://doi.org/10.1371/journal.pgen.1009860

Imbalanced segregation of recombinant haplotypes in hybrid populations reveals inter- and intrachromosomal Dobzhansky-Muller incompatibilities

Juan Li, Molly Schumer, Claudia Bank

PLOS Genetics: published March 28, 2022 | https://doi.org/10.1371/journal.pgen.1010120

Dendrite regeneration in C. elegans is controlled by the RAC GTPase CED-10 and the RhoGEF TIAM-1

Harjot Kaur Brar, Swagata Dey, Smriti Bhardwaj, Devashish Pande, Pallavi Singh, Shirshendu Dey, Anindya Ghosh-Roy

PLOS Genetics: published March 28, 2022 | https://doi.org/10.1371/journal.pgen.1010127

The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae

Leonardo F. Lemos Rocha, Katharina Peters, Jacob Biboy, Jamie S. Depelteau, Ariane Briegel, Waldemar Vollmer, Melanie Blokesch

PLOS Genetics: published March 28, 2022 | https://doi.org/10.1371/journal.pgen.1010143

Phage-inducible chromosomal islands promote genetic variability by blocking phage reproduction and protecting transductants from phage lysis

Rodrigo Ibarra-Chávez, Aisling Brady, John Chen, José R. Penadés, Andreas F. Haag

PLOS Genetics: published March 28, 2022 | https://doi.org/10.1371/journal.pgen.1010146

RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells

Xinxin Peng, Yikai Luo, Hongyue Li, Xuejiao Guo, Hu Chen, Xuwo Ji, Han Liang

PLOS Genetics: published March 30, 2022 | https://doi.org/10.1371/journal.pgen.1010130

Rare and common variants in ROM1 and PRPH2 genes trans-modify Stargardt/ABCA4 disease

Jana Zernant, Winston Lee, Jun Wang, Kerry Goetz, Ehsan Ullah, Takayuki Nagasaki, Pei-Yin Su, Gerald A. Fishman, Stephen H. Tsang, Santa J. Tumminia, Brian P. Brooks, Robert B. Hufnagel, Rui Chen, Rando Allikmets

PLOS Genetics: published March 30, 2022 | https://doi.org/10.1371/journal.pgen.1010129

Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection

David Peris, Dabao Sun Lu, Vilde Bruhn Kinneberg, Ine-Susanne Methlie, Malin Stapnes Dahl, Timothy Y. James, Håvard Kauserud, Inger Skrede

PLOS Genetics: published March 31, 2022 | https://doi.org/10.1371/journal.pgen.1010097

Correction: Analysis of HubP-dependent cell pole protein targeting in Vibrio cholerae uncovers novel motility regulators

The PLOS Genetics Staff

PLOS Genetics: published March 1, 2022 | https://doi.org/10.1371/journal.pgen.1010094

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PLOS Genetics: published March 15, 2022 | https://doi.org/10.1371/journal.pgen.1010125

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THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data

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PLOS Genetics: published March 8, 2022 | https://doi.org/10.1371/journal.pgen.1010102