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Table of Contents

June 2019 | Volume 2, No. 3

Research Articles

  • Noncoding AUG circRNAs constitute an abundant and conserved subclass of circles
    Open Access
    Noncoding AUG circRNAs constitute an abundant and conserved subclass of circles

    Lotte VW Stagsted, Katrine M Nielsen, Iben Daugaard, Thomas B Hansen

    Lotte VW Stagsted ... Thomas B Hansen

    Published 26 April 2019

    AUG circRNAs are highly abundant and conserved with an Alu-independent mode of biogenesis. Although AUG circRNAs contain the N-terminal ORFs, no evidence supports translation of these circRNAs.

  • Characterisation of class VI TRIM RING domains: linking RING activity to C-terminal domain identity
    Open Access
    Characterisation of class VI TRIM RING domains: linking RING activity to C-terminal domain identity

    Rebecca V Stevens, Diego Esposito, Katrin Rittinger

    Rebecca V Stevens ... Katrin Rittinger

    Published 26 April 2019

    This study shows that members of the class VI TRIM E3 ligase family contain monomeric RING domains and display no ligase activity and may require additional regulatory events to promote ubiquitination.

  • Cellular response upon proliferation in the presence of an active mitotic checkpoint
    Open Access
    Cellular response upon proliferation in the presence of an active mitotic checkpoint

    Andrea Corno, Elena Chiroli, Fridolin Gross, Claudio Vernieri, Vittoria Matafora, Stefano Maffini, Marco Cosentino Lagomarsino, Angela Bachi, Andrea Ciliberto

    Andrea Corno ... Andrea Ciliberto

    Published 8 May 2019

    Cells that replicate with an active mitotic checkpoint remain capable to mount multiple times an efficient arrest, are bigger than unperturbed cells, rely more heavily on Cdh1, and have an altered protein expression profile.

  • Chitinase 1 regulates pulmonary fibrosis by modulating TGF-β/SMAD7 pathway via TGFBRAP1 and FOXO3
    Open Access
    Chitinase 1 regulates pulmonary fibrosis by modulating TGF-β/SMAD7 pathway via TGFBRAP1 and FOXO3

    Chang-Min Lee, Chuan-Hua He, Jin Wook Park, Jae Hyun Lee, Suchita Kamle, Bing Ma, Bedia Akosman, Roberto Cotez, Emily Chen, Yang Zhou, Erica L Herzog, Changwan Ryu, Xueyan Peng, Ivan O Rosas, Sergio Poli, Carol Feghali Bostwick, Augustine M Choi, Jack A Elias, Chun Geun Lee

    Chang-Min Lee ... Chun Geun Lee

    Published 13 May 2019

    Chitinase 1 (CHIT1) plays a role in the pathogenesis of pulmonary fibrosis by modulating canonical and noncanonical TGF-β signaling via interaction with TGFBRAP1 and FOXO3. These findings highlight the CHIT1/SMAD7 axis as a potential biomarker and therapeutic target of pulmonary fibrosis.

  • MicroRNA-155 is essential for the optimal proliferation and survival of plasmablast B cells
    Open Access
    MicroRNA-155 is essential for the optimal proliferation and survival of plasmablast B cells

    Giuseppina Arbore, Tom Henley, Laura Biggins, Simon Andrews, Elena Vigorito, Martin Turner, Rebecca Leyland

    Giuseppina Arbore ... Rebecca Leyland

    Published 16 May 2019

    Tracking antigen-specific B cells in vivo since the onset of antigen stimulation shows that miR-155 regulates the early expansion of B-blasts and later on the optimal proliferation and survival of plasmablasts in a B-cell–intrinsic manner.

  • An N-terminal–truncated isoform of FAM134B (FAM134B-2) regulates starvation-induced hepatic selective ER-phagy
    Open Access
    An N-terminal–truncated isoform of FAM134B (FAM134B-2) regulates starvation-induced hepatic selective ER-phagy

    Shohei Kohno, Yuji Shiozaki, Audrey L Keenan, Shinobu Miyazaki-Anzai, Makoto Miyazaki

    Shohei Kohno ... Makoto Miyazaki

    Published 17 May 2019

    This study has identified a novel truncated isoform of FAM134B (FAM134B-2) that regulates starvation-induced selective ER-phagy of secretory proteins such as ApoCIII through the activation of C/EBPβ.

  • Loss of PGC-1α in RPE induces mesenchymal transition and promotes retinal degeneration
    Open Access
    Loss of PGC-1α in RPE induces mesenchymal transition and promotes retinal degeneration

    Mariana Aparecida Brunini Rosales, Daisy Y Shu, Jared Iacovelli, Magali Saint-Geniez

    Mariana Aparecida Brunini Rosales ... Magali Saint-Geniez

    Published 17 May 2019

    Sustained loss of PGC-1α in RPE cells triggers mitochondrial/autophagic dysfunction and oxidative damage resulting in epithelial dedifferentiation and mesenchymal transition. RPE dysfunction caused by deletion of the PGC-1 coactivators in vivo causes retinal degeneration.

  • The hypoxia-response pathway modulates RAS/MAPK–mediated cell fate decisions in <em>Caenorhabditis elegans</em>
    Open Access
    The hypoxia-response pathway modulates RAS/MAPK–mediated cell fate decisions in Caenorhabditis elegans

    Sabrina Maxeiner, Judith Grolleman, Tobias Schmid, Jan Kammenga, Alex Hajnal

    Sabrina Maxeiner ... Alex Hajnal

    Published 24 May 2019

    Atmospheric oxygen levels modulate the RAS/MAPK signaling pathway in the nematode Caenorhabditis elegans through a cross-talk between the DELTA/NOTCH and hypoxia signaling pathways. These mechanisms may permit the animals to adapt their development to changes in the environment.

  • Molecular characterization of CHAD domains as inorganic polyphosphate-binding modules
    Open Access
    Molecular characterization of CHAD domains as inorganic polyphosphate-binding modules

    Laura Lorenzo-Orts, Ulrich Hohmann, Jinsheng Zhu, Michael Hothorn

    Laura Lorenzo-Orts ... Michael Hothorn

    Published 27 May 2019

    A domain of unknown function termed CHAD, present in all kingdoms of life, is characterized as a specific inorganic polyphosphate-binding domain.

  • Rate of brain aging and <em>APOE ε4</em> are synergistic risk factors for Alzheimer’s disease
    Open Access
    Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer’s disease

    Christin A Glorioso, Andreas R Pfenning, Sam S Lee, David A Bennett, Etienne L Sibille, Manolis Kellis, Leonard P Guarente

    Christin A Glorioso ... Leonard P Guarente

    Published 27 May 2019

    This study describes a gauge for brain aging predictive of cognitive decline and Alzheimer's disease synergistic with the APOE ε4 allele.

  • Tumor-intrinsic response to IFNγ shapes the tumor microenvironment and anti–PD-1 response in NSCLC
    Open Access
    Tumor-intrinsic response to IFNγ shapes the tumor microenvironment and anti–PD-1 response in NSCLC

    Bonnie L Bullock, Abigail K Kimball, Joanna M Poczobutt, Alexander J Neuwelt, Howard Y Li, Amber M Johnson, Jeff W Kwak, Emily K Kleczko, Rachael E Kaspar, Emily K Wagner, Katharina Hopp, Erin L Schenk, Mary CM Weiser-Evans, Eric T Clambey, Raphael A Nemenoff

    Bonnie L Bullock ... Raphael A Nemenoff

    Published 27 May 2019

    Using an immunocompetent mouse model of NSCLC, this study demonstrates that tumor-intrinsic response to IFNγ determines response to anti–PD-1 through alterations in the tumor microenvironment.

  • PKAc is not required for the preerythrocytic stages of <em>Plasmodium berghei</em>
    Open Access
    PKAc is not required for the preerythrocytic stages of Plasmodium berghei

    Hadi Hasan Choudhary, Roshni Gupta, Satish Mishra

    Hadi Hasan Choudhary ... Satish Mishra

    Published 29 May 2019

    The mutant salivary gland sporozoites lacking PKAc are able to glide, invade hepatocytes, and mature into hepatic merozoites, which release successfully from the merosome, however, fail to initiate blood stage infection when inoculated into mice.

  • The <em>S</em>. Typhi effector StoD is an E3/E4 ubiquitin ligase which binds K48- and K63-linked diubiquitin
    Open Access
    The S. Typhi effector StoD is an E3/E4 ubiquitin ligase which binds K48- and K63-linked diubiquitin

    Melanie A McDowell, Alexander MP Byrne, Elli Mylona, Rebecca Johnson, Agnes Sagfors, Valerie F Crepin, Susan Lea, Gad Frankel

    Melanie A McDowell ... Gad Frankel

    Published 29 May 2019

    Salmonella Typhi is estimated to cause 100,000–200,000 deaths annually, yet its infection strategy remains elusive. This article reports of the first Typhi-specific effector, which has an E3/E4 ubiquitin ligase activity and can uniquely bind K48- and K63-linked diubiquitin.

  • The m<sup>6</sup>A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants
    Open Access
    The m6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants

    Dominique Pontier, Claire Picart, Moaine El Baidouri, François Roudier, Tao Xu, Sylvie Lahmy, Christel Llauro, Jacinthe Azevedo, Michèle Laudié, Aurore Attina, Christophe Hirtz, Marie-Christine Carpentier, Lisha Shen, Thierry Lagrange

    Dominique Pontier ... Thierry Lagrange

    Published 29 May 2019

    This study reveals that an m6A-assisted polyadenylation pathway comprising conserved m6A writer proteins and a plant-specific m6A reader contributes to transcriptome integrity in Arabidopsis thaliana by restricting RNA chimera formation at rearranged loci.

  • Mesenchymal stromal cell activation by breast cancer secretomes in bioengineered 3D microenvironments
    Open Access
    Mesenchymal stromal cell activation by breast cancer secretomes in bioengineered 3D microenvironments

    Ulrich Blache, Edward R Horton, Tian Xia, Erwin M Schoof, Lene H Blicher, Angelina Schönenberger, Jess G Snedeker, Ivan Martin, Janine T Erler, Martin Ehrbar

    Ulrich Blache ... Martin Ehrbar

    Published 3 June 2019

    This study shows the activation of tumour-associated mesenchymal stromal cells by breast cancer secretomes in bioengineered 3D microenvironments using comprehensive multiomics analysis methods.

  • Robust repression of tRNA gene transcription during stress requires protein arginine methylation
    Open Access
    Robust repression of tRNA gene transcription during stress requires protein arginine methylation

    Richoo B Davis, Neah Likhite, Christopher A Jackson, Tao Liu, Michael C Yu

    Richoo B Davis ... Michael C Yu

    Published 3 June 2019

    This work examines how protein arginine methylation of Rpc31, a subunit of RNA Pol III, promotes negative regulation of tRNA biogenesis in the context of cellular stress.

  • Opposing functions of F-BAR proteins in neuronal membrane protrusion, tubule formation, and neurite outgrowth
    Open Access
    Opposing functions of F-BAR proteins in neuronal membrane protrusion, tubule formation, and neurite outgrowth

    Kendra L Taylor, Russell J Taylor, Karl E Richters, Brandon Huynh, Justin Carrington, Maeve E McDermott, Rebecca L Wilson, Erik W Dent

    Kendra L Taylor ... Erik W Dent

    Published 3 June 2019

    Neurite formation is a fundamental antecedent to axon and dendrite formation, but the mechanisms that underlie this important process are poorly characterized. Here, we demonstrate that two F-BAR proteins, CIP4 and FBP17, have opposing functions in early cortical neuron development.

  • ATP hydrolysis by KaiC promotes its KaiA binding in the cyanobacterial circadian clock system
    Open Access
    ATP hydrolysis by KaiC promotes its KaiA binding in the cyanobacterial circadian clock system

    Yasuhiro Yunoki, Kentaro Ishii, Maho Yagi-Utsumi, Reiko Murakami, Susumu Uchiyama, Hirokazu Yagi, Koichi Kato

    Yasuhiro Yunoki ... Koichi Kato

    Published 3 June 2019

    ATP hydrolysis in the KaiC hexamer triggers the exposure of its C-terminal segments into the solvent so as to capture KaiA, providing mechanistic insights into the circadian periodicity regulation.

  • Molecular characterization of <em>Chlamydomonas reinhardtii</em> telomeres and telomerase mutants
    Open Access
    Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants

    Stephan Eberhard, Sona Valuchova, Julie Ravat, Jaroslav Fulneček, Pascale Jolivet, Sandrine Bujaldon, Stéphane D Lemaire, Francis-André Wollman, Maria Teresa Teixeira, Karel Riha, Zhou Xu

    Stephan Eberhard ... Zhou Xu

    Published 3 June 2019

    This study characterizes the sequence, end structure, and length distribution of Chlamydomonas reinhardtii telomeres and shows that telomerase mutants are defective in telomere maintenance.

  • The WT1–BASP1 complex is required to maintain the differentiated state of taste receptor cells
    Open Access
    The WT1–BASP1 complex is required to maintain the differentiated state of taste receptor cells

    Yankun Gao, Debarghya Dutta Banik, Mutia M Muna, Stefan GE Roberts, Kathryn F Medler

    Yankun Gao ... Kathryn F Medler

    Published 5 June 2019

    The WT1/BASP1 complex is important to maintain taste receptor cells in their terminally differentiated state.

  • Evidence for vesicle-mediated antigen export by the human pathogen <em>Babesia microti</em>
    Open Access
    Evidence for vesicle-mediated antigen export by the human pathogen Babesia microti

    Jose Thekkiniath, Nicole Kilian, Lauren Lawres, Meital A Gewirtz, Morven M Graham, Xinran Liu, Michel Ledizet, Choukri Ben Mamoun

    Jose Thekkiniath ... Choukri Ben Mamoun

    Published 13 June 2019

    The human pathogen Babesia microti undergoes unique morphogenesis during its development within human and mouse red blood cells and uses a novel vesicle-based system for export of antigens into the host cell and environment.

  • CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms
    Open Access
    CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms

    Erich Brunner, Ryohei Yagi, Marc Debrunner, Dezirae Beck-Schneider, Alexa Burger, Eliane Escher, Christian Mosimann, George Hausmann, Konrad Basler

    Erich Brunner ... Konrad Basler

    Published 13 June 2019

    CRISPR–Cas9 enables recombination between homologous chromosome arms at predefined sites and also underscores the need for caution when applying CRISPR technologies in translational medicine.

  • Expression of a constitutively active human <em>STING</em> mutant in hematopoietic cells produces an <em>Ifnar1</em>-dependent vasculopathy in mice
    Open Access
    Expression of a constitutively active human STING mutant in hematopoietic cells produces an Ifnar1-dependent vasculopathy in mice

    Gary R Martin, Kimiora Henare, Carolina Salazar, Teresa Scheidl-Yee, Laura J Eggen, Pankaj P Tailor, Jung Hwan Kim, John Podstawka, Marvin J Fritzler, Margaret M Kelly, Bryan G Yipp, Frank R Jirik

    Gary R Martin ... Frank R Jirik

    Published 20 June 2019

    Transgenic expression of a mutant hSTING cDNA under the control of the Vav1 gene promoter leads to a vasculopathy similar to that of the interferonopathy, STING-associated vasculopathy of infancy.

  • An unusual and vital protein with guanylate cyclase and P4-ATPase domains in a pathogenic protist
    Open Access
    An unusual and vital protein with guanylate cyclase and P4-ATPase domains in a pathogenic protist

    Özlem Günay-Esiyok, Ulrike Scheib, Matthias Noll, Nishith Gupta

    Özlem Günay-Esiyok ... Nishith Gupta

    Published 24 June 2019

    Toxoplasma gondii harbors an alveolate-specific guanylate cyclase linked to P-type ATPase motifs, which is an essential actuator of cGMP-dependent gliding motility, egress, and invasion during acute infection.

  • Fibro-adipogenic progenitors of dystrophic mice are insensitive to NOTCH regulation of adipogenesis
    Open Access
    Fibro-adipogenic progenitors of dystrophic mice are insensitive to NOTCH regulation of adipogenesis

    Milica Marinkovic, Claudia Fuoco, Francesca Sacco, Andrea Cerquone Perpetuini, Giulio Giuliani, Elisa Micarelli, Theodora Pavlidou, Lucia Lisa Petrilli, Alessio Reggio, Federica Riccio, Filomena Spada, Simone Vumbaca, Alessandro Zuccotti, Luisa Castagnoli, Matthias Mann, Cesare Gargioli, Gianni Cesareni

    Milica Marinkovic ... Gianni Cesareni

    Published 25 June 2019

    The NOTCH pathway, in concert with TNFa, restrains adipogenesis of muscle fibro-adipogenic progenitors (FAPs). Dystrophin-deficient FAPs are less sensitive to NOTCH anti-adipogenic signals, thus explaining why fat infiltrations are solely observed in the muscles of dystrophic individuals.

  • Tamoxifen blocks retrograde trafficking of Shiga toxin 1 and 2 and protects against lethal toxicosis
    Open Access
    Tamoxifen blocks retrograde trafficking of Shiga toxin 1 and 2 and protects against lethal toxicosis

    Andrey S Selyunin, Steven Hutchens, Stanton F McHardy, Somshuvra Mukhopadhyay

    Andrey S Selyunin ... Somshuvra Mukhopadhyay

    Published 26 June 2019

    This study reports an unexpected role of late endosome–lysosome fusion in early endosome-to-Golgi trafficking of Shiga toxins and identifies tamoxifen to be a potent inhibitor of Shiga toxicosis.

  • Assembly mechanisms of the bacterial cytoskeletal protein FilP
    Open Access
    Assembly mechanisms of the bacterial cytoskeletal protein FilP

    Ala Javadi, Niklas Söderholm, Annelie Olofsson, Klas Flärdh, Linda Sandblad

    Ala Javadi ... Linda Sandblad

    Published 26 June 2019

    FilP is a coiled-coil protein that self-assembles into striated filaments and meshwork that shares structural and biochemical characteristics with metazoan intermediate filaments.

Resource

  • Development of a new monoclonal antibody specific to mouse Vγ6 chain
    Open Access
    Development of a new monoclonal antibody specific to mouse Vγ6 chain

    Shinya Hatano, Xin Tun, Naoto Noguchi, Dan Yue, Hisakata Yamada, Xun Sun, Mitsuru Matsumoto, Yasunobu Yoshikai

    Shinya Hatano ... Yasunobu Yoshikai

    Published 7 May 2019

    Using a novel mAb specific to Vγ6 TCR, we find Vγ6+ γδT cells are located in association with medullary thymic epithelial cells and play crucial roles in protection against Klebsiella pneumoniae infection but are pathogenic in psoriasis-like dermatitis in agreement with earlier studies.

Correction

  • Open Access
    Correction: Loss of PGC-1α in RPE induces mesenchymal transition and promotes retinal degeneration

    Mariana Aparecida Brunini Rosales, Daisy Y Shu, Jared Iacovelli, Magali Saint-Geniez

    Mariana Aparecida Brunini Rosales ... Magali Saint-Geniez

    Published 29 May 2019
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Volume 2, No. 3
June 2019
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