Table of Contents
Volume 37, Number 6, 15 March 2018
News & Views
- No way out: when RNA elements promote nuclear retention
The proper localization of RNA transcripts is a highly controlled and fine‐tuned process. Indeed, regulation of RNA trafficking is mediated by both cis‐acting elements and trans‐acting factors, and defects in either mechanism have been associated with disease. Identifying the RNA sequence motifs that determine cellular localization for a given transcript therefore represents an important and challenging task. A new study from Shukla et al in The EMBO Journal—along with related work from Lubelsky and Ulitsky published elsewhere—describes a new screen that uses hybrid RNAs with barcoded oligonucleotides to identify cis‐acting elements that increase the propensity of RNAs to be retained in the nuclear compartment.
See also: CJ Shukla et al (March 2018)
High‐throughput RNA oligo tiling provides a new method for testing functional domains in long noncoding RNAs, shedding light on this diverse and poorly understood group of transcripts.
The EMBO Journal (2018) 37: e99123
- © 2018 The Authors
Resource
- High‐throughput identification of RNA nuclear enrichment sequences
- Chinmay J Shukla1,2,3,4,
- Alexandra L McCorkindale1,5,
- Chiara Gerhardinger1,2,
- Keegan D Korthauer3,6,
- Moran N Cabili2,
- David M Shechner1,2,
- Rafael A Irizarry3,6,
- Philipp G Maass1,† and
- John L Rinn (john.rinn{at}colorado.edu)*,1,2,7,8,†
- 1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- 2Broad Institute of MIT and Harvard, Cambridge, MA, USA
- 3Department of Biostatistics and Computational Biology, Dana‐Farber Cancer Institute, Boston, MA, USA
- 4Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
- 5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- 6Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- 7Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- 8Present Address: Department of Biochemistry, University of Colorado BioFrontiers, Boulder, CO, USA
- ↵*Corresponding author. Tel: +1 303 735 7218; E‐mail: john.rinn{at}colorado.edu
↵† These authors contributed equally to this work
A new tiling‐based method maps functional domains across a panel of long non‐coding RNAs, identifying sequence motifs that retain these RNAs in the nucleus.
Synopsis
A new tiling‐based method maps functional domains in RNAs in a high‐throughput manner, allowing the identification of sequence motifs that contribute to the nuclear enrichment of long non‐coding RNAs.
Massively Parallel RNA Assay (MPRNA) is a universally applicable method to survey RNA‐based functionalities in a high‐throughput manner.
MPRNA identifies 109 nuclear enrichment sequences across 29 of 38 lncRNAs tested.
A C‐rich motif is generally enriched in nuclear versus cytoplasmic transcripts.
RNA‐FISH Fish reveals that large sequence domains are sufficient to localize otherwise cytoplasmic RNA to the nucleus.
MPRNA shows that nuclear lncRNAs have unique and large (˜500 bp) nuclear localization domains
The EMBO Journal (2018) 37: e98452
- Received October 19, 2017.
- Revision received December 18, 2017.
- Accepted December 20, 2017.
- © 2018 The Authors. Published under the terms of the CC BY 4.0 license
This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Articles
- LPS targets host guanylate‐binding proteins to the bacterial outer membrane for non‐canonical inflammasome activation
- José Carlos Santos1,2,
- Mathias S Dick1,
- Brice Lagrange3,
- Daniel Degrandi4,
- Klaus Pfeffer4,
- Masahiro Yamamoto5,
- Etienne Meunier6,
- Pawel Pelczar7,
- Thomas Henry3 and
- Petr Broz (petr.broz{at}unil.ch)*,1,2
- 1Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
- 2Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
- 3Centre International de Recherche en Infectiologie, Inserm U1111, CNRS, UMR 5308, Université Claude Bernard Lyon‐1 Ecole Normale Supérieure, Lyon, France
- 4Institute of Medical Microbiology and Hospital Hygiene, Heinrich‐Heine‐University Düsseldorf, Düsseldorf, Germany
- 5Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- 6Institute of Pharmacology and Structural Biology (IPBS), University of Toulouse, Toulouse Cedex 04, France
- 7Center for Transgenic Models, University of Basel, Basel, Switzerland
- ↵*Corresponding author. Tel: +41 21 692 56 56; E‐mail: petr.broz{at}unil.ch
Immunogenicity of bacterial outer membrane vesicles is linked to lipopolysaccharide delivery and TLR4‐TRIF signaling in host macrophages.
Synopsis
Cytosolic immune detection of LPS in mouse macrophages is promoted by guanylate‐binding proteins (GBPs) that associate with LPS‐containing membranes and hereby promote the interaction of LPS to caspase‐11, which is constitutes the non‐canonical inflammasome.
Bacterial OMVs induce production of type‐I interferons through TLR4‐TRIF signaling, triggering expression of cytosolic GBPs.
Isoprenylated GBPs are recruited to cytosolic OMVs, which drives activation of the caspase‐11 non‐canonical inflammasome.
LPS is the key factor of the outer bacterial membrane that promotes GBP recruitment and GBP‐dependent inflammasome activation.
GBPs also facilitate caspase‐11 binding to transfected cytosolic bacterial LPS.
In vivo, GBPs promote endotoxic shock induced by OMV‐derived LPS.
The EMBO Journal (2018) 37: e98089
- Received August 25, 2017.
- Revision received January 17, 2018.
- Accepted January 19, 2018.
- © 2018 The Authors
- Prion‐like protein aggregates exploit the RHO GTPase to cofilin‐1 signaling pathway to enter cells
- Zhen Zhong1,
- Laura Grasso1,†,
- Caroline Sibilla1,†,
- Tim J Stevens1,
- Nicholas Barry1 and
- Anne Bertolotti (aberto{at}mrc-lmb.cam.ac.uk)*,1
- ↵*Corresponding author. Tel: +44 1223 267054; E‐mail: aberto{at}mrc-lmb.cam.ac.uk
↵† These authors contributed equally to this work
RNAi screening shows that pathological protein aggregates harness a signaling pathway also utilized by viruses to remodel cortical actin and invade host cells.
Synopsis
Protein aggregates associated with neurodegenerative diseases can penetrate cells and spread like prions. Results from an RNAi screen show that pathological protein aggregates exploit signaling and cytoskeleton‐remodeling pathways also used by viruses to enter host cells.
Mutant SOD1 protein aggregates use cofilin‐1 to remodel actin and invade host cells.
Signaling through RHO GTPase, ROCK1 and LIMK1 to cofilin‐1 remodels actin to facilitate aggregate entry.
Cofilin‐1 activity is altered in the spinal cord of SOD1G93A transgenic mice.
Tau and α‐synuclein aggregates also exploit RHO GTPase signaling to cofilin‐1 to enter cells.
The EMBO Journal (2018) 37: e97822
- Received July 20, 2017.
- Revision received January 16, 2018.
- Accepted January 24, 2018.
- © 2018 MRC Laboratory of Molecular Biology
- Molecular basis for sterol transport by StART‐like lipid transfer domains
- Florian A Horenkamp1,†,
- Diana P Valverde1,†,
- Jodi Nunnari2 and
- Karin M Reinisch (karin.reinisch{at}yale.edu)*,1
- 1Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- 2Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
- ↵*Corresponding author. Tel: +1 203 785 6469; E‐mail: karin.reinisch{at}yale.edu
↵† These authors contributed equally to this work
Mammalian LAM family proteins have StART‐like lipid transfer domains, transferring sterols efficiently. The structure of the lipid transfer module of a yeast LAM protein reveals how StART proteins bind sterol.
Synopsis
Mammalian LAM family proteins have StART‐like lipid transfer domains, transferring sterols efficiently. The structure of the lipid transfer module of a yeast LAM protein reveals how StART proteins bind sterol.
Mammalian proteins in the LAM family (GramD1a‐c) transfer sterols with similar efficiency as known sterol transporters.
GramD1b also transfers PI(4,5)P2 in vitro.
Sterol binds yeast LAM protein near the opening of the ligand binding cavity, with water occupying the cavity base.
The EMBO Journal (2018) 37: e98002
- Received August 14, 2017.
- Revision received February 2, 2018.
- Accepted February 5, 2018.
- © 2018 The Authors
- A single nucleotide incorporation step limits human telomerase repeat addition activity
- Yinnan Chen1,†,
- Joshua D Podlevsky1,†,
- Dhenugen Logeswaran1 and
- Julian J‐L Chen (jlchen{at}asu.edu)*,1
- ↵*Corresponding author. Tel: +1 480 965 3650; E‐mail: jlchen{at}asu.edu
↵† These authors contributed equally to this work
A template‐encoded pause‐signal links processive repeat addition of human telomerase to cellular nucleotide levels.
Synopsis
The single incorporation step of the first dG nucleotide in the human telomerase catalytic cycle is inhibited by the template‐embedded pause signal, limiting processive repeat addition. High dGTP alleviates this restricted step and stimulates repeat addition processivity and rate.
The human telomerase template‐embedded pause signal has dual functions.
The template‐embedded pause signal induces a high KM for the first dG nucleotide incorporation.
The first nucleotide incorporation mediates dGTP stimulation of telomerase repeat addition.
Human telomerase can utilize deoxynucleoside diphosphates as substrate.
The EMBO Journal (2018) 37: e97953
- Received August 8, 2017.
- Revision received November 30, 2017.
- Accepted January 5, 2018.
- © 2018 The Authors
- Structural basis of siRNA recognition by TRBP double‐stranded RNA binding domains
- Gregoire Masliah1,
- Christophe Maris1,
- Sebastian LB König2,
- Maxim Yulikov3,
- Florian Aeschimann4,
- Anna L Malinowska5,
- Julie Mabille4,
- Jan Weiler4,
- Andrea Holla2,
- Juerg Hunziker4,
- Nicole Meisner‐Kober4,
- Benjamin Schuler2,
- Gunnar Jeschke3 and
- Frederic H‐T Allain (allain{at}mol.biol.ethz.ch)*,1
- 1Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
- 2Department of Biochemistry, University of Zürich, Zürich, Switzerland
- 3Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
- 4Novartis Institutes for Biomedical Research, Basel, Switzerland
- 5Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
- ↵*Corresponding author. Tel: +41 44 633 39 40; E‐mail: allain{at}mol.biol.ethz.ch
NMR studies of the dsRNA‐binding protein TRBP suggest that its role in facilitating miRNA biogenesis is to increase accuracy of the Dicer RNase.
Synopsis
RNA‐binding protein TRBP associates with RNase Dicer to facilitate miRNA biogenesis. An NMR structure of TRBP's dsRNA binding domains shows that TRBP and Dicer bind pre‐miRNAs on opposite sides during processing, suggesting that TRBP works by increasing Dicer accuracy rather than strand selection.
The double‐stranded RNA binding domains (dsRBDs) of TRBP do not sense siRNA asymmetry.
The TRBP dsRBDs bind an asymmetric siRNA in two symmetric, equally populated, orientations.
There is no competition for pre‐miRNA binding between the TRBP dsRBDs and Dicer.
The EMBO Journal (2018) 37: e97089
- Received April 11, 2017.
- Revision received January 10, 2018.
- Accepted January 12, 2018.
- © 2018 The Authors. Published under the terms of the CC BY 4.0 license
This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
- HP1α targets the chromosomal passenger complex for activation at heterochromatin before mitotic entry
- Jan G Ruppert1,
- Kumiko Samejima1,
- Melpomeni Platani1,
- Oscar Molina1,4,
- Hiroshi Kimura2,
- A Arockia Jeyaprakash1,
- Shinya Ohta3 and
- William C Earnshaw (bill.earnshaw{at}ed.ac.uk)*,1
- 1Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
- 2Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- 3Department of Biochemistry, Medical School, Kochi University, Nankoku, Kochi, Japan
- 4Present Address: Josep Carreras Leukaemia Research Institute, School of Medicine, University of Barcelona, Barcelona, Spain
- ↵*Corresponding author. Tel: +44 131 650 7101; E‐mail: bill.earnshaw{at}ed.ac.uk
Tethering experiments and detection of H3S10 phosphorylation in G2 suggest that HP1 initially clusters the chromosomal passenger complex for activation, before other epigenetic marks determine its cent localisation in mitosis.
Synopsis
This study highlights a robust interaction between HP1 and the chromosomal passenger complex (CPC) in cells. H3S10 phosphorylation foci in G2, a result of CPC activity, depend on HP1α/HP1γ, suggesting that HP1 initially clusters the CPC for activation before other epigenetic marks determine its localisation in mitosis.
HP1α tethering shows a robust interaction between HP1α and the CPC in cells.
The CPC clustered at HP1 foci is catalytically active even in interphase.
H3S10 phosphorylation foci appear in G2 before H3T3 phosphorylation and are independent of CDK1 activity.
HP1α and HP1γ are involved in clustering and activating the CPC in G2 phase.
The EMBO Journal (2018) 37: e97677
- Received June 26, 2017.
- Revision received January 24, 2018.
- Accepted January 29, 2018.
- © 2018 The Authors. Published under the terms of the CC BY 4.0 license
This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
