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Table of Contents

January 2023 | Volume 6, No. 1

Research Articles

  • Exploratory meta-analysis of hypoxic transcriptomes using a precise transcript reference sequence set
    Open Access
    Exploratory meta-analysis of hypoxic transcriptomes using a precise transcript reference sequence set

    Yoko Ono, Hidemasa Bono

    Yoko Ono ... Hidemasa Bono

    Published 10 October 2022

    Exploratory meta-analysis of hypoxic RNA-seq data using FANTOM-CAT as a reference transcriptome facilitates the evaluation of relationship between sense–antisense transcripts from the same locus.

  • A dominant negative mitofusin causes mitochondrial perinuclear clusters because of aberrant tethering
    Open Access
    A dominant negative mitofusin causes mitochondrial perinuclear clusters because of aberrant tethering

    Stephanie R Sloat, Suzanne Hoppins

    Stephanie R Sloat ... Suzanne Hoppins

    Published 13 October 2022

    Our analysis of a CMT2A-associated mitofusin variant reveals that aberrant mitochondrial tethering results in perinuclear clusters and that conformational dynamics in Hinge 2 are required to progress from membrane tethering to membrane fusion.

  • Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication
    Open Access
    Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication

    Tobias Moll, Valerie Odon, Calum Harvey, Mark O Collins, Andrew Peden, John Franklin, Emily Graves, Jack NG Marshall, Cleide dos Santos Souza, Sai Zhang, Lydia Castelli, Guillaume Hautbergue, Mimoun Azzouz, David Gordon, Nevan Krogan, Laura Ferraiuolo, Michael P Snyder, Pamela J Shaw, Jan Rehwinkel, Johnathan Cooper-Knock

    Tobias Moll ... Johnathan Cooper-Knock

    Published 14 October 2022

    Genetic evidence and in vitro experiments with live virus suggest EXOSC2 depletion can reduce SARS-CoV-2 replication without significant toxicity.

  • The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import
    Open Access
    The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import

    Saskia Rödl, Fabian den Brave, Markus Räschle, Büsra Kizmaz, Svenja Lenhard, Carina Groh, Hanna Becker, Jannik Zimmermann, Bruce Morgan, Elke Richling, Thomas Becker, Johannes M Herrmann

    Saskia Rödl ... Johannes M Herrmann

    Published 17 October 2022

    Yeast cells employ the cytosolic ubiquitin system to increase the capacity of the mitochondrial import machinery during phases of metabolic transitions.

  • Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution
    Open Access
    Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution

    Matko Glunčić, Ines Vlahović, Marija Rosandić, Vladimir Paar

    Matko Glunčić ... Vladimir Paar

    Published 19 October 2022

    The human genome, unlike the genomes of other primates, contains tandemly organized higher order NBPF structures that represent a link to the development of their cognitive abilities.

  • A prediction model for COVID-19 liver dysfunction in patients with normal hepatic biochemical parameters
    Open Access
    A prediction model for COVID-19 liver dysfunction in patients with normal hepatic biochemical parameters

    Jianfeng Bao, Shourong Liu, Xiao Liang, Congcong Wang, Lili Cao, Zhaoyi Li, Furong Wei, Ai Fu, Yingqiu Shi, Bo Shen, Xiaoli Zhu, Yuge Zhao, Hong Liu, Liangbin Miao, Yi Wang, Shuang Liang, Linyan Wu, Jinsong Huang, Tiannan Guo, Fang Liu

    Jianfeng Bao ... Fang Liu

    Published 19 October 2022

    The composite model of sex and the novel protein marker ANGL3 exhibits great potential in predicting the risk of developing LD in COVID-19 patients with normal hepatic biochemical parameters on admission.

  • Replication-associated inversions are the dominant form of bacterial chromosome structural variation
    Open Access
    Replication-associated inversions are the dominant form of bacterial chromosome structural variation

    Matthew D’Iorio, Ken Dewar

    Matthew D’Iorio ... Ken Dewar

    Published 19 October 2022

    Prokaryotic rearrangements symmetric to the replication origin are identified across 247 bacterial species. Large-scale inversions are found to be highly prevalent across species, and their mediating factors are examined. The full pipeline and dataset are available on GitHub at https://github.com/mdiorio371/RASR.

  • An inducible amphipathic α-helix mediates subcellular targeting and membrane binding of RPE65
    Open Access
    An inducible amphipathic α-helix mediates subcellular targeting and membrane binding of RPE65

    Sheetal Uppal, Tingting Liu, Emily Galvan, Fatima Gomez, Tishina Tittley, Eugenia Poliakov, Susan Gentleman, T Michael Redmond

    Sheetal Uppal ... T Michael Redmond

    Published 20 October 2022

    Amino acid residues 107–125 of RPE65, in concert with a palmitoyl group at C112, form a membrane-sensing amphipathic helix that targets RPE65 to smooth endoplasmic reticulum to acquire its substrate.

  • Dlk1-Dio3 cluster miRNAs regulate mitochondrial functions in the dystrophic muscle in Duchenne muscular dystrophy
    Open Access
    Dlk1-Dio3 cluster miRNAs regulate mitochondrial functions in the dystrophic muscle in Duchenne muscular dystrophy

    Ai Vu Hong, Nathalie Bourg, Peggy Sanatine, Jerome Poupiot, Karine Charton, Evelyne Gicquel, Emmanuelle Massourides, Marco Spinazzi, Isabelle Richard, David Israeli

    Ai Vu Hong ... David Israeli

    Published 20 October 2022

    A large number of DLK1-DIO3 miRNAs are up-regulated in the muscles and the serum of Duchenne muscular dystrophy, animal models, and patients. Mitochondrial functions, and in particular oxidative phosphorylation, are targeted by these coordinately up-regulated DLK1-DIO3 miRNAs.

  • MDF is a conserved splicing factor and modulates cell division and stress response in <em>Arabidopsis</em>
    Open Access
    MDF is a conserved splicing factor and modulates cell division and stress response in Arabidopsis

    Cloe de Luxán-Hernández, Julia Lohmann, Eduardo Tranque, Jana Chumova, Pavla Binarova, Julio Salinas, Magdalena Weingartner

    Cloe de Luxán-Hernández ... Magdalena Weingartner

    Published 20 October 2022

    MDF acts like its human homolog SART1 as a splicing factor that is important for maintenance of genome stability and correct splicing and expression of genes involved in cell division and stress response.

  • Stepwise progression of β-selection during T cell development involves histone deacetylation
    Open Access
    Stepwise progression of β-selection during T cell development involves histone deacetylation

    Anchi S Chann, Mirren Charnley, Lucas M Newton, Andrea Newbold, Florian Wiede, Tony Tiganis, Patrick O Humbert, Ricky W Johnstone, Sarah M Russell

    Anchi S Chann ... Sarah M Russell

    Published 25 October 2022

    T cells undergoing beta-selection differentiate via sequential expression of co-receptors CD28, CD5, and CD2, exposing new signalling controls that are disrupted by a cancer therapeutic.

  • Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish
    Open Access
    Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish

    Barbara Uszczynska-Ratajczak, Sreedevi Sugunan, Monika Kwiatkowska, Maciej Migdal, Silvia Carbonell-Sala, Anna Sokol, Cecilia L Winata, Agnieszka Chacinska

    Barbara Uszczynska-Ratajczak ... Agnieszka Chacinska

    Published 25 October 2022

    The vast majority (99%) of mitochondrial proteins are encoded by the nuclear genome, synthesized in the cytosol and imported into the organelle. Here we study the principles of mitochondrial import in vivo from the RNA perspective using zebrafish.

  • Actin-binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II
    Open Access
    Actin-binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin II

    Yuuki Hayakawa, Masak Takaine, Kien Xuan Ngo, Taiga Imai, Masafumi D Yamada, Arash Badami Behjat, Kenichi Umeda, Keiko Hirose, Ayhan Yurtsever, Noriyuki Kodera, Kiyotaka Tokuraku, Osamu Numata, Takeshi Fukuma, Toshio Ando, Kentaro Nakano, Taro QP Uyeda

    Yuuki Hayakawa ... Taro QP Uyeda

    Published 26 October 2022

    Rng2CHD, an actin-binding domain of an IQGAP, induces cooperative conformational changes in actin filaments and inhibits movement driven by myosin II.

  • Miro GTPase domains regulate the assembly of the mitochondrial motor–adaptor complex
    Open Access
    Miro GTPase domains regulate the assembly of the mitochondrial motor–adaptor complex

    Kayla Davis, Himanish Basu, Ismael Izquierdo-Villalba, Ethan Shurberg, Thomas L Schwarz

    Kayla Davis ... Thomas L Schwarz

    Published 27 October 2022

    Relocalizing the mitochondrial motor–adaptor protein Miro to peroxisomes and systematically manipulating each GTPase domain reveal the importance of the N-terminal GTPase domain of Miro1 for regulating mitochondrial transport.

  • Palmitate impairs circadian transcriptomics in muscle cells through histone modification of enhancers
    Open Access
    Palmitate impairs circadian transcriptomics in muscle cells through histone modification of enhancers

    Nicolas J Pillon, Laura Sardón Puig, Ali Altıntaş, Prasad G Kamble, Salvador Casaní-Galdón, Brendan M Gabriel, Romain Barrès, Ana Conesa, Alexander V Chibalin, Erik Näslund, Anna Krook, Juleen R Zierath

    Nicolas J Pillon ... Juleen R Zierath

    Published 27 October 2022

    The disruption of circadian rhythms because of lipid overload may lead to epigenomic changes that influence metabolism. Thus, a dietary or therapeutic modulation of lipid levels, a cornerstone in the treatment of metabolic disorders, may prevent circadian misalignment in peripheral tissues.

  • circEXOC5 promotes acute lung injury through the PTBP1/Skp2/Runx2 axis to activate autophagy
    Open Access
    circEXOC5 promotes acute lung injury through the PTBP1/Skp2/Runx2 axis to activate autophagy

    Pei Gao, Beirong Wu, Ying Ding, Bingru Yin, Haoxiang Gu

    Pei Gao ... Haoxiang Gu

    Published 27 October 2022

    circEXOC5 activates autophagy and promotes acute lung injury via stimulating the Skp2 decay to stabilize Runx2 by interacting with PTBP1.

  • In vivo probing of SECIS-dependent selenocysteine translation in Archaea
    Open Access
    In vivo probing of SECIS-dependent selenocysteine translation in Archaea

    Nils Peiter, Michael Rother

    Nils Peiter ... Michael Rother

    Published 31 October 2022

    By turning a bacterial reporter into an archaeal selenoprotein, in vivo probing of structure–function relations during UGA recoding for selenoprotein synthesis in Archaea is greatly facilitated.

  • CRISPRi screening reveals regulators of tau pathology shared between exosomal and vesicle-free tau
    Open Access
    CRISPRi screening reveals regulators of tau pathology shared between exosomal and vesicle-free tau

    Juan Carlos Polanco, Yevhen Akimov, Avinash Fernandes, Adam Briner, Gabriel Rhys Hand, Marloes van Roijen, Giuseppe Balistreri, Jürgen Götz

    Juan Carlos Polanco ... Jürgen Götz

    Published 31 October 2022

    Using a genome-wide CRISPRi screen, we identified ANKLE2, BANF1, NUSAP1, EIF1AD, and VPS18 as novel regulators of tau pathology induced by both exosome-like extracellular vesicles and free tau seeds.

  • Tanshinone functions as a coenzyme that confers gain of function of NQO1 to suppress ferroptosis
    Open Access
    Tanshinone functions as a coenzyme that confers gain of function of NQO1 to suppress ferroptosis

    Tian-Xiang Wang, Kun-Long Duan, Zi-Xuan Huang, Zi-An Xue, Jun-Yun Liang, Yongjun Dang, Ao Zhang, Yue Xiong, Chunyong Ding, Kun-Liang Guan, Hai-Xin Yuan

    Tian-Xiang Wang ... Hai-Xin Yuan

    Published 1 November 2022

    NQO1 catalyzes the reduction of tanshinones to detoxify lipid peroxyl radicals and inhibit ferroptosis both in vitro and in vivo, providing a molecular mechanism for the therapeutic effects of tanshinones, such as cardiac protection.

  • The potential of a universal influenza virus-like particle vaccine expressing a chimeric cytokine
    Open Access
    The potential of a universal influenza virus-like particle vaccine expressing a chimeric cytokine

    Kuniaki Nerome, Toshifumi Imagawa, Shigeo Sugita, Youta Arasaki, Kenichi Maegawa, Kazunori Kawasaki, Tsuyoshi Tanaka, Shinji Watanabe, Hidekazu Nishimura, Tetsuro Suzuki, Kazumichi Kuroda, Isao Kosugi, Zenta Kajiura

    Kuniaki Nerome ... Zenta Kajiura

    Published 7 November 2022

    Herein, a virus-like particle vaccine with chimeric cytokine shows the protective efficacy against different strains of influenza virus, laying the foundation for designing a universal influenza vaccine.

  • Lack of peroxisomal catalase affects heat shock response in <em>Caenorhabditis elegans</em>
    Open Access
    Lack of peroxisomal catalase affects heat shock response in Caenorhabditis elegans

    Marina Musa, Pedro A Dionisio, Ricardo Casqueiro, Ira Milosevic, Nuno Raimundo, Anita Krisko

    Marina Musa ... Anita Krisko

    Published 8 November 2022

    The authors present a previously unknown crosstalk between peroxisomes and the heat shock response, whereby the peroxisomal catalase is vital for cellular capacity to survive heat stress and undergo heat-induced lifespan extension.

  • C-to-U RNA deamination is the driving force accelerating SARS-CoV-2 evolution
    Open Access
    C-to-U RNA deamination is the driving force accelerating SARS-CoV-2 evolution

    Yan Li, Fanghua Hou, Meili Zhou, Xiaoping Yang, Bin Yin, Wenqing Jiang, Huiqing Xu

    Yan Li ... Huiqing Xu

    Published 8 November 2022

    The authors propose that the host-mediated C-to-U RNA editing event, which is also affected by the RNA structure, is the driving force that accelerates SARS-CoV-2 mutation and evolution.

  • LACTB exerts tumor suppressor properties in epithelial ovarian cancer through regulation of Slug
    Open Access
    LACTB exerts tumor suppressor properties in epithelial ovarian cancer through regulation of Slug

    Valentina Cutano, Jessica Marianne Ferreira Mendes, Sara Escudeiro-Lopes, Susana Machado, Judith Vinaixa Forner, Juan M Gonzales-Morena, Martin Prevorovsky, Viacheslav Zemlianski, Yuxiong Feng, Petra Kralova Viziova, Andrea Hartmanova, Beata Malcekova, Pavel Jakoube, Sonia Iyer, Zuzana Keckesova

    Valentina Cutano ... Zuzana Keckesova

    Published 14 November 2022

    We show the ability of LACTB to function as a tumor suppressor in ovarian cancer through down-regulation of Slug and induction of differentiation.

  • Lipid saturation induces degradation of squalene epoxidase for sterol homeostasis and cell survival
    Open Access
    Lipid saturation induces degradation of squalene epoxidase for sterol homeostasis and cell survival

    Leng-Jie Huang, Rey-Huei Chen

    Leng-Jie Huang ... Rey-Huei Chen

    Published 11 November 2022

    The authors describe the ER-associated degradation of Erg1 under increased membrane lipid saturation and show its importance in balancing sterol levels for membrane integrity in budding yeast.

  • Loss of autism-candidate CHD8 perturbs neural crest development and intestinal homeostatic balance
    Open Access
    Loss of autism-candidate CHD8 perturbs neural crest development and intestinal homeostatic balance

    Gaëlle Hayot, Mathieu Massonot, Céline Keime, Elodie Faure, Christelle Golzio

    Gaëlle Hayot ... Christelle Golzio

    Published 14 November 2022

    A combination of zebrafish and transcriptomic analyses revealed the role of the autism-candidate chd8 in the development of the enteric nervous system, serotonin metabolism, and intestinal integrity.

  • Discovery of RUF6 ncRNA–interacting proteins involved in <em>P. falciparum</em> immune evasion
    Open Access
    Discovery of RUF6 ncRNA–interacting proteins involved in P. falciparum immune evasion

    Gretchen M Diffendall, Anna Barcons-Simon, Sebastian Baumgarten, Florent Dingli, Damarys Loew, Artur Scherf

    Gretchen M Diffendall ... Artur Scherf

    Published 15 November 2022

    An RNA-directed proteomic discovery (ChIRP-MS) protocol is used to identify in vivo RUF6 ncRNA–protein interactions that sustain virulence genes in the human malaria parasite, Plasmodium falciparum.

  • SMA-linked SMN mutants prevent phase separation properties and SMN interactions with FMRP family members
    Open Access
    SMA-linked SMN mutants prevent phase separation properties and SMN interactions with FMRP family members

    Olivier Binda, Franceline Juillard, Julia Novion Ducassou, Constance Kleijwegt, Geneviève Paris, Andréanne Didillon, Faouzi Baklouti, Armelle Corpet, Yohann Couté, Jocelyn Côté, Patrick Lomonte

    Olivier Binda ... Patrick Lomonte

    Published 14 November 2022

    The survival motor neuron (SMN) protein associates with translation regulators and phase-separates into RNA-stabilized droplets that are likely candidates for the formation of nuclear and cytoplasmic membraneless organelles.

  • Endoplasmic reticulum membranes are continuously required to maintain mitotic spindle size and forces
    Open Access
    Endoplasmic reticulum membranes are continuously required to maintain mitotic spindle size and forces

    Margarida Araújo, Alexandra Tavares, Diana V Vieira, Ivo A Telley, Raquel A Oliveira

    Margarida Araújo ... Raquel A Oliveira

    Published 15 November 2022

    Using microinjection approaches in Drosophila embryos, Araújo et al reveal that acute disruption of the ER at centrosome-proximal sites perturbs the architecture of the mitotic spindle, with a direct impact on nuclear positioning.

  • ZBTB18 inhibits SREBP-dependent lipid synthesis by halting CTBPs and LSD1 activity in glioblastoma
    Open Access
    ZBTB18 inhibits SREBP-dependent lipid synthesis by halting CTBPs and LSD1 activity in glioblastoma

    Roberto Ferrarese, Annalisa Izzo, Geoffroy Andrieux, Simon Lagies, Johanna Paulina Bartmuss, Anie Priscilla Masilamani, Alix Wasilenko, Daniela Osti, Stefania Faletti, Rana Schulzki, Shuai Yuan, Eva Kling, Valentino Ribecco, Dieter Henrik Heiland, Stefan Tholen, Marco Prinz, Giuliana Pelicci, Bernd Kammerer, Melanie Boerries, Maria Stella Carro

    Roberto Ferrarese ... Maria Stella Carro

    Published 22 November 2022

    This study identifies a new mechanism of fatty acid synthesis regulation in glioblastoma that involves ZBTB18, CTBP, and LSD1. The transcriptional repressor ZBTB18 interacts with CTBP and inhibits LSD1 demethylase activity.

  • GPER1 links estrogens to centrosome amplification and chromosomal instability in human colon cells
    Open Access
    GPER1 links estrogens to centrosome amplification and chromosomal instability in human colon cells

    Miriam Bühler, Jeanine Fahrländer, Alexander Sauter, Markus Becker, Elisa Wistorf, Matthias Steinfath, Ailine Stolz

    Miriam Bühler ... Ailine Stolz

    Published 16 November 2022

    This study reveals a causal link between (xeno)estrogen-activated GPER1, centriole-positive numerical centrosome amplification, and genomic instability in normal colon and colorectal cancer cells.

  • Hepatic DKK1-driven steatosis is CD36 dependent
    Open Access
    Hepatic DKK1-driven steatosis is CD36 dependent

    Zhen Yang, Xinping Huang, Jiaye Zhang, Kai You, Yue Xiong, Ji Fang, Anteneh Getachew, Ziqi Cheng, Xiaorui Yu, Yan Wang, Feima Wu, Ning Wang, Shufen Feng, Xianhua Lin, Fan Yang, Yan Chen, Hongcheng Wei, Yin-xiong Li

    Zhen Yang ... Yin-xiong Li

    Published 21 November 2022

    Increased DKK1 in hepatic steatosis contributes CD36-mediated fatty acid uptake and insulin resistance.

Resources

  • Myeloma immunoglobulin rearrangement and translocation detection through targeted capture sequencing
    Open Access
    Myeloma immunoglobulin rearrangement and translocation detection through targeted capture sequencing

    Signy Chow, Olena Kis, David T Mulder, Arnavaz Danesh, Jeff Bruce, Ting Ting Wang, Donna Reece, Nizar Bhalis, Paola Neri, Peter JB Sabatini, Jonathan Keats, Suzanne Trudel, Trevor J Pugh

    Signy Chow ... Trevor J Pugh

    Published 3 November 2022

    Targeted capture sequencing (CapIG-seq) is a novel, efficient, and effective approach to examine multiple genomic alterations in ctDNA and bone marrow aspirates of patients with multiple myeloma.

  • Protein and RNA ADP-ribosylation detection is influenced by sample preparation and reagents used
    Open Access
    Protein and RNA ADP-ribosylation detection is influenced by sample preparation and reagents used

    Lisa Weixler, Nonso Josephat Ikenga, Jim Voorneveld, Gülcan Aydin, Timo MHR Bolte, Jeffrey Momoh, Mareike Bütepage, Alexandra Golzmann, Bernhard Lüscher, Dmitri V Filippov, Roko Žaja, Karla LH Feijs

    Lisa Weixler ... Karla LH Feijs

    Published 11 November 2022

    Mono(ADP-ribosyl)ation is an emerging modification, for which recently detection reagents were generated. We cross-validated all reagents and observe remarkable differences in efficiency, depending on the substrate investigated and on the methods that are used.

  • Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing
    Open Access
    Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

    Jonathan Liu, Vanessa Tran, Venkata Naga Pranathi Vemuri, Ashley Byrne, Michael Borja, Yang Joon Kim, Snigdha Agarwal, Ruofan Wang, Kyle Awayan, Abhishek Murti, Aris Taychameekiatchai, Bruce Wang, George Emanuel, Jiang He, John Haliburton, Angela Oliveira Pisco, Norma F Neff

    Jonathan Liu ... Norma F Neff

    Published 16 December 2022

    Single-cell RNA-seq is an important technology for capturing gene expression in individual cells. It has limitations as spatial context and accurate representation of cell types in the tissue are lost. Here, we show that MERFISH is comparable to scRNA-seq.

Methods

  • A high-content endogenous GLUT4 trafficking assay reveals new aspects of adipocyte biology
    Open Access
    A high-content endogenous GLUT4 trafficking assay reveals new aspects of adipocyte biology

    Alexis Diaz-Vegas, Dougall M Norris, Sigrid Jall-Rogg, Kristen C Cooke, Olivia J Conway, Amber S Shun-Shion, Xiaowen Duan, Meg Potter, Julian van Gerwen, Harry JM Baird, Sean J Humphrey, David E James, Daniel J Fazakerley, James G Burchfield

    Alexis Diaz-Vegas ... James G Burchfield

    Published 25 October 2022

    The authors describe a high-throughput method for measuring endogenous GLUT4 and transferrin receptor translocation in adipocytes. They reveal that this method has advantages over studying GLUT4 trafficking using overexpressed GLUT4 reporters, which are commonly used in the field.

  • Genome-wide profiling of histone modifications in <em>Plasmodium falciparum</em> using CUT&amp;RUN
    Open Access
    Genome-wide profiling of histone modifications in Plasmodium falciparum using CUT&RUN

    Riward Campelo Morillo, Chantal T Harris, Kit Kennedy, Samuel R Henning, Björn FC Kafsack

    Riward Campelo Morillo ... Björn FC Kafsack

    Published 15 November 2022

    We present a detailed step-wise protocol for reliable genome-wide profiling of histone modifications using CUT&RUN that requires only low numbers of Plasmodium falciparum blood stages.

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Volume 6, No. 1
January 2023
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