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Table of Contents

01 December 2013; volume 14, issue 12

Upfront

Science & Society

Review

  • Building and remodelling Cullin–RING E3 ubiquitin ligases
    1. John R Lydeard1,
    2. Brenda A Schulman2 and
    3. J Wade Harper*,1
    1. 1 Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA
    2. 2 Departments of Structural Biology and Tumour Cell Biology, Howard Hughes Medical Institute, St Jude Children's Research Hospital, Memphis, Tennessee, 38105, USA
    1. ↵*Corresponding author. Tel: (617) 432‐6590; Fax: (617) 432‐6591; E-mail: wade_harper{at}hms.harvard.edu

    Cullin‐RING E3 ubiquitin ligases (CRLs) are multiprotein complexes that ubiquitylate a plethora of signalling proteins, thereby broadly affecting cellular processes. This review is focused on how CRLs are dynamically controlled, with an emphasis on neddylation cycles and substrate receptor exchange.

    • cullin
    • ubiquitin
    • Nedd8
    • COP9 signalosome
    • E3 ligase
    • CAND1
    • Received September 3, 2013.
    • Accepted October 8, 2013.
    John R Lydeard, Brenda A Schulman, J Wade Harper
    Published online 01.12.2013
  • Cellular dynamics in the muscle satellite cell niche
    1. C Florian Bentzinger1,
    2. Yu Xin Wang1,2,
    3. Nicolas A Dumont1 and
    4. Michael A Rudnicki*,1,2
    1. 1 Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada
    2. 2 Faculty of Medicine, Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
    1. ↵*Corresponding author. Tel: 00 1 (613) 739 6740; Fax: 00 1 (613) 739 6294; E-mail: mrudnicki{at}ohri.ca

    Multiple, functionally diverse cell types have been shown to contribute to skeletal muscle regeneration. This Review discusses the cellular dynamics and the roles of immune, fibrogenic, vessel‐associated and myogenic cells in the response of the satellite cell niche to muscle injury and disease.

    • skeletal muscle satellite cells
    • muscle stem cell niche
    • accessory cell types
    • myogenic cell types
    • muscular dystrophy
    • Received September 5, 2013.
    • Accepted October 21, 2013.
    C Florian Bentzinger, Yu Xin Wang, Nicolas A Dumont, Michael A Rudnicki
    Published online 01.12.2013
  • Open Access
    Three wise centromere functions: see no error, hear no break, speak no delay
    1. Tomoyuki U Tanaka*,1,
    2. Lesley Clayton1 and
    3. Toyoaki Natsume1,2
    1. 1 Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
    2. 2 Present address: Molecular Function Laboratory, Centre for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan
    1. ↵*Corresponding author. Tel: +44‐1382‐385814; Fax: +44‐1382‐386375; E-mail: t.tanaka{at}dundee.ac.uk

    Centromeres are known to promote kinetochore assembly. However, two other roles—facilitating robust sister chromatid cohesion and advancing the replication timing of centromeric regions—have recently emerged. The three are analysed in this Review.

    • centromere
    • kinetochore
    • microtubule attachment
    • sister‐kinetochore bi‐orientation
    • sister‐chromatid cohesion
    • DNA replication timing
    • Received September 5, 2013.
    • Accepted October 18, 2013.

    This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Tomoyuki U Tanaka, Lesley Clayton, Toyoaki Natsume
    Published online 01.12.2013

Scientific Reports

  • Open Access
    PARP1 orchestrates variant histone exchange in signal‐mediated transcriptional activation
    1. Amanda O'Donnell1,
    2. Shen‐Hsi Yang1 and
    3. Andrew D Sharrocks*,1
    1. 1 Faculty of Life Sciences, University of Manchester, Manchester, UK
    1. ↵*Corresponding author. Tel:+44 (0)161 275 5979; Fax:+44 (0)161 275 5082; E-mail: a.d.sharrocks{at}man.ac.uk

    This study reveals an essential role for PARP1 in the exchange of the histone variant H2A.Z by H2A at the ‐1 nucleosome of the FOS promoter, which promotes signal‐induced transcriptional activation.

    • chromatin
    • H2A.Z
    • immediate early genes
    • MAP kinase signalling
    • PARP
    • Received August 2, 2013.
    • Accepted September 16, 2013.

    This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Amanda O'Donnell, Shen‐Hsi Yang, Andrew D Sharrocks
    Published online 01.12.2013
  • No need for a power stroke in ISWI‐mediated nucleosome sliding
    1. Johanna Ludwigsen1,
    2. Henrike Klinker1,2 and
    3. Felix Mueller‐Planitz*,1
    1. 1 Adolf‐Butenandt‐Institute, Ludwig‐Maximilians‐Universität, 80336, Munich, Germany
    2. 2 Center for Integrated Protein Science Munich, Ludwig‐Maximilians‐Universität, Munich, Germany
    1. ↵*Corresponding author. Tel:+089 2180 75 431; Fax:+089 2180 75 425; E-mail: felix.mueller-planitz{at}med.uni-muenchen.de

    Nucleosome remodellers are thought to mechanically pull extranucleosomal DNA into the nucleosome. Surprisingly, even when the mechanical step is experimentally prevented, ISWI can still reposition nucleosomes. The authors discuss alternative models to explain the mechanism.

    • ISWI
    • chromatin remodelling
    • nucleosome sliding
    • Received July 23, 2013.
    • Revision received September 4, 2013.
    • Accepted September 16, 2013.
    Johanna Ludwigsen, Henrike Klinker, Felix Mueller‐Planitz
    Published online 01.12.2013
  • Nucleosome sliding by Chd1 does not require rigid coupling between DNA‐binding and ATPase domains
    1. Ilana M Nodelman1 and
    2. Gregory D Bowman*,1
    1. 1 T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
    1. ↵*Corresponding author. Tel:+1 410 516 7850; Fax:+1 410 516 4118; E-mail: gdbowman{at}jhu.edu

    Chromatin remodellers are thought to require a rigid connection between ATPase and DNA‐binding domain to reposition nucleosomes. However, the linking segment of Chd1 can accommodate large changes in length and flexibility, showing that current models for remodeller activity must be revised.

    • Chd1
    • chromatin remodeller
    • nucleosome sliding
    • Received July 24, 2013.
    • Revision received September 11, 2013.
    • Accepted September 17, 2013.
    Ilana M Nodelman, Gregory D Bowman
    Published online 01.12.2013
  • hPrimpol1/CCDC111 is a human DNA primase‐polymerase required for the maintenance of genome integrity
    1. Li Wan1,†,
    2. Jiangman Lou1,†,
    3. Yisui Xia2,†,
    4. Bei Su1,
    5. Ting Liu1,
    6. Jiamin Cui2,
    7. Yingying Sun1,
    8. Huiqiang Lou*,2 and
    9. Jun Huang*,1
    1. 1 Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, 310058, China
    2. 2 State key laboratory of Agro‐Biotechnology, College of Biological Sciences, Agricultural University, Beijing, 100193, China
    1. ↵*Corresponding authors. Tel:+86 10 6273 4504; Fax:+86 10 6273 4504; E-mail: lou{at}cau.edu.cn or Tel:+86 571 8898 1391; Fax:+86 571 8898 1391; E-mail: jhuang{at}zju.edu.cn

    1. ↵† These authors contributed equally to this work.

    This study identifies the first human DNA primase‐polymerase, which is required for stalled replication fork restart and the maintenance of genome integrity.

    • hPrimpol1/CCDC111
    • primase‐polymerase
    • RPA1
    • stalled replication fork
    • Received July 25, 2013.
    • Revision received September 17, 2013.
    • Accepted September 17, 2013.
    Li Wan, Jiangman Lou, Yisui Xia, Bei Su, Ting Liu, Jiamin Cui, Yingying Sun, Huiqiang Lou, Jun Huang
    Published online 01.12.2013
  • Open Access
    Tpo1‐mediated spermine and spermidine export controls cell cycle delay and times antioxidant protein expression during the oxidative stress response
    1. Antje Krüger1,2,
    2. Jakob Vowinckel1,
    3. Michael Mülleder1,
    4. Phillip Grote2,
    5. Floriana Capuano1,
    6. Katharina Bluemlein1,† and
    7. Markus Ralser*,1,3
    1. 1 Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK
    2. 2 Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
    3. 3 Division of Physiology and Metabolism, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
    1. ↵*Corresponding author. Tel:+44 (0)1223 761346; Fax:+44 (0)1223 766002; E-mail: mr559{at}cam.ac.uk

    • ↵† Present address: Quotient Bioresearch, CB7 5WW Fordham, Cambridgeshire, UK

    Cellular export of the metabolites spermine and spermidine is induced under oxidative stress to control the timing of antioxidant gene expression and cell cycle delay and to promote cell survival.

    • oxidative stress response
    • polyamines
    • cell cycle arrest
    • metabolite export
    • timing
    • Received August 29, 2013.
    • Revision received September 20, 2013.
    • Accepted September 20, 2013.

    This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    Antje Krüger, Jakob Vowinckel, Michael Mülleder, Phillip Grote, Floriana Capuano, Katharina Bluemlein, Markus Ralser
    Published online 01.12.2013
  • Interaction with both ZNRF3 and LGR4 is required for the signalling activity of R‐spondin
    1. Yang Xie1,†,
    2. Raffaella Zamponi1,
    3. Olga Charlat1,
    4. Melissa Ramones1,
    5. Susanne Swalley1,
    6. Xiaomo Jiang1,
    7. Daniel Rivera1,
    8. William Tschantz1,
    9. Bo Lu1,
    10. Lisa Quinn1,
    11. Chris Dimitri1,
    12. Jefferson Parker1,
    13. Doug Jeffery1,
    14. Sheri K Wilcox2,
    15. Mike Watrobka2,
    16. Peter LeMotte1,
    17. Brian Granda1,
    18. Jeffrey A Porter1,
    19. Vic E Myer1,
    20. Andreas Loew1 and
    21. Feng Cong*,1
    1. 1 Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts, 02139, USA
    2. 2 SomaLogic, Inc., 2945 Wilderness Place, Boulder Colorado, 80301, USA
    1. ↵*Corresponding author. Tel:+1 617 871 7510; Fax:+1 617 871 7262; E-mail: feng.cong{at}novartis.com

    • ↵† Present address: FORMA Therapeutics, Inc., 500 Arsenal Street, Watertown, Massachusetts 02472, USA.

    This study shows that both ZNRF3‐ and LGR4‐binding motifs of R‐spondin are required for its Wnt‐promoting activity. These results support a dual receptor model of R‐spondin signalling, where LGR4 serves as the engagement receptor while ZNRF3 functions as the effector receptor.

    • Wnt
    • R‐spondin; ZNRF3
    • RNF43
    • LGR4
    • Received June 18, 2013.
    • Revision received October 1, 2013.
    • Accepted October 1, 2013.
    Yang Xie, Raffaella Zamponi, Olga Charlat, Melissa Ramones, Susanne Swalley, Xiaomo Jiang, Daniel Rivera, William Tschantz, Bo Lu, Lisa Quinn, Chris Dimitri, Jefferson Parker, Doug Jeffery, Sheri K Wilcox, Mike Watrobka, Peter LeMotte, Brian Granda, Jeffrey A Porter, Vic E Myer, Andreas Loew, Feng Cong
    Published online 01.12.2013
  • Open Access
    Loss of iron triggers PINK1/Parkin‐independent mitophagy
    1. George F G Allen1,
    2. Rachel Toth1,
    3. John James2 and
    4. Ian G Ganley*,1
    1. 1 MRC‐Protein Phosphorylation and Ubiquitylation Unit
    2. 2 Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
    1. ↵*Corresponding author. Tel:+01382 388905; Fax:+01382 223778; E-mail: i.ganley{at}dundee.ac.uk

    A novel mitophagy assay uncovers a new PINK1/Parkin‐independent mitophagy pathway induced by a decrease in iron levels. This pathway is active in fibroblasts of Parkinson patients with Parkin mutations and could be exploited as a potential therapy.

    • autophagy
    • iron/mitophagy
    • PINK1
    • Parkin
    • Received June 4, 2013.
    • Revision received September 30, 2013.
    • Accepted October 1, 2013.

    This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

    George F G Allen, Rachel Toth, John James, Ian G Ganley
    Published online 01.12.2013
  • Tightly controlled WRKY23 expression mediates Arabidopsis embryo development
    1. Wim Grunewald*,1,2,†,
    2. Ive De Smet*,1,2,3,†,
    3. Bert De Rybel4,
    4. Helene S Robert1,2,
    5. Brigitte van de Cotte1,2,
    6. Viola Willemsen5,
    7. Godelieve Gheysen6,
    8. Dolf Weijers4,
    9. Jiří Friml1,2 and
    10. Tom Beeckman1,2
    1. 1 Department of Plant Systems Biology, VIB, and Bioinformatics, Ghent University, 9052, Ghent, Belgium
    2. 2 Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
    3. 3 Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, LE12 5RD, Loughborough, UK
    4. 4 Laboratory of Biochemistry, Wageningen University, 6703 HA, Wageningen, The Netherlands
    5. 5 Plant Developmental Biology Wageningen University, 6700 AP, Wageningen, The Netherlands
    6. 6 Department Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium
    1. ↵*Corresponding authors. Tel:+32 92446611; Fax:+32 92446610; E-mail: wim.grunewald{at}vib.be or Tel:+32 93313890; Fax:+32 93313809; E-mail: ive.desmet{at}psb.vib-ugent.be

    1. ↵† These authors contributed equally to this work.

    This study presents evidence that the tightly controlled expression of the transcription factor WRKY23 regulates both auxin‐dependent and auxin‐independent signalling pathways leading to root stem cell niche specification in Arabidopsis.

    • Arabidopsis
    • embryogenesis
    • WRKY
    • Received March 21, 2013.
    • Revision received October 4, 2013.
    • Accepted October 4, 2013.
    Wim Grunewald, Ive De Smet, Bert De Rybel, Helene S Robert, Brigitte van de Cotte, Viola Willemsen, Godelieve Gheysen, Dolf Weijers, Jiří Friml, Tom Beeckman
    Published online 01.12.2013
  • Piezo1‐dependent stretch‐activated channels are inhibited by Polycystin‐2 in renal tubular epithelial cells
    1. Rémi Peyronnet1,†,
    2. Joana R Martins1,†,
    3. Fabrice Duprat1,
    4. Sophie Demolombe1,
    5. Malika Arhatte1,
    6. Martine Jodar1,
    7. Michel Tauc2,
    8. Christophe Duranton2,
    9. Marc Paulais3,
    10. Jacques Teulon3,
    11. Eric Honoré*,1 and
    12. Amanda Patel1
    1. 1 Institut de Pharmacologie Moléculaire et Cellulaire, LabEx ICST, UMR 7275 CNRS, Université de Nice Sophia Antipolis, Valbonne, France
    2. 2 CNRS‐FRE 472, Laboratoire de Physiomédecine Moléculaire, Université de Nice Sophia Antipolis, Nice, France
    3. 3 UPMC Université Paris 06, UMR 872 CNRS, Laboratoire de Génomique, Physiologie et Physiopathologie Rénales, Paris, France
    1. ↵*Corresponding author. Tel:+33 493 957745; Fax:+33 493 957704; E-mail: honore{at}ipmc.cnrs.fr

    1. ↵† These authors contributed equally to this work.

    This study provides evidence that the activity of renal non‐selective stretch‐activated ion channels (SACs) depends on Piezo1 but is negatively regulated by Polycystin‐2 (PC2). PC2 co‐immunoprecipitates with Piezo1 and deletion of its N‐terminal domain prevents both this interaction and inhibition of SAC activity.

    • Fam38A
    • kidney
    • Piezo1
    • PKD
    • mechanotransduction
    • TRP channels
    • Received May 6, 2013.
    • Revision received October 7, 2013.
    • Accepted October 7, 2013.
    Rémi Peyronnet, Joana R Martins, Fabrice Duprat, Sophie Demolombe, Malika Arhatte, Martine Jodar, Michel Tauc, Christophe Duranton, Marc Paulais, Jacques Teulon, Eric Honoré, Amanda Patel
    Published online 01.12.2013
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In this Issue
Volume 14, Number 12
01 December 2013
EMBO reports: 14 (12)
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