RNA Biology
- RNA activation‐independent DNA targeting of the Type III CRISPR‐Cas system by a Csm complex
- Kwang‐Hyun Park1,
- Yan An1,
- Tae‐Yang Jung2,3,4,
- In‐Young Baek1,
- Haemin Noh2,
- Woo‐Chan Ahn1,2,
- Hans Hebert3,4,
- Ji‐Joon Song2,
- Jeong‐Hoon Kim5,
- Byung‐Ha Oh (bhoh{at}kaist.ac.kr)*,2 and
- Eui‐Jeon Woo (ejwoo{at}kribb.re.kr)*,1,6
- 1Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- 2Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST) Institute for the BioCentury, Daejeon, South Korea
- 3Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- 4School of Technology and Health, KTH Royal Institute of Technology, Huddinge, Sweden
- 5Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- 6Department of Analytical Bioscience, University of Science and Technology, Daejeon, South Korea
- ↵*
Corresponding author. Tel: +82 423502648; E‐mail: bhoh{at}kaist.ac.kr
Corresponding author. Tel: +82 428798432; E‐mail: ejwoo{at}kribb.re.kr
The Type III CRISPR‐Cas system in T. onnurineus cleaves target ssDNA in a direct cis‐acting and target RNA‐independent manner, suggesting a novel ssDNA targeting mechanism of the Type III system.
Synopsis
The Type III CRISPR‐Cas system in T. onnurineus cleaves target ssDNA in a direct cis‐acting and target RNA‐independent manner, suggesting a novel ssDNA targeting mechanism of the Type III system.
The Csm effector complex of T. onnurineus was reconstituted with a minimalistic combination of Csm1121334151.
The complex shows RNA targeting and RNA‐activated ssDNA targeting activities.
The complex shows RNA activation‐independent ssDNA targeting activity that requires the HD domain of the Csm1 subunit.
EMBO Reports (2017) 18: 826–840
- Received November 20, 2016.
- Revision received February 19, 2017.
- Accepted February 23, 2017.
- © 2017 The Authors
- Nuclear retention of the lncRNA SNHG1 by doxorubicin attenuates hnRNPC–p53 protein interactions
- Yuan Shen1,2,†,
- Shanshan Liu1,3,†,
- Jiao Fan1,4,
- Yinghua Jin (yhjin{at}jlu.edu.cn)*,3,
- Baolei Tian1,
- Xiaofei Zheng (xfzheng100{at}126.com)*,1 and
- Hanjiang Fu (fuhj75{at}126.com)*,1
- 1Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
- 2Department of Advanced Interdisciplinary Studies, Institute of Basic Medical Sciences and Tissue Engineering Research Center, Beijing Institute of Basic Medical Sciences, Beijing, China
- 3Key Laboratory for Molecular Enzymology and Engineering (The Ministry of Education), College of Life Sciences, Jilin University, Changchun, Jilin, China
- 4Institute of Geriatrics, Chinese PLA General Hospital, Beijing, China
- ↵*
Corresponding author. Tel: +86 431 85155221; E‐mail: yhjin{at}jlu.edu.cn
Corresponding author. Tel: +86 10 68214653; E‐mail: xfzheng100{at}126.com
Corresponding author. Tel: +86 10 66931237; Fax: +86 10 80705115; E‐mail: fuhj75{at}126.com
↵† These authors contributed equally to this work
p53 is a crucial regulator of cellular responses to toxic stress. This study identifies hnRNPC as a destabilizing p53 regulator. Doxorubicin treatment induces the nuclear retention and subsequent interaction of the lncRNA SNHG1 with hnRNPC, which impairs p53 destabilization.
Synopsis
p53 is a crucial regulator of cellular responses to toxic stress. This study identifies hnRNPC as a destabilizing p53 regulator. Doxorubicin treatment induces the nuclear retention and subsequent interaction of the lncRNA SNHG1 with hnRNPC, which impairs p53 destabilization.
The ribonucleoprotein hnRNPC directly binds to p53.
The hnRNPC interaction destabilizes p53 and prevents its activation.
Doxorubicin treatment retains the lncRNA SNHG1 in the nucleus through its binding with nucleolin.
Nuclear SNHG1 traps hnRNPC, which stabilizes p53 and promotes p53‐dependent apoptosis.
EMBO Reports (2017) 18: 536–548
- Received July 29, 2016.
- Revision received January 26, 2017.
- Accepted February 6, 2017.
- © 2017 The Authors
- MicroRNA‐independent functions of DGCR8 are essential for neocortical development and TBR1 expression
- Federica Marinaro1,
- Matteo J Marzi2,
- Nadin Hoffmann1,
- Hayder Amin1,
- Roberta Pelizzoli1,
- Francesco Niola1,
- Francesco Nicassio2 and
- Davide De Pietri Tonelli (davide.depietri{at}iit.it)*,1
- 1Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
- 2Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
- ↵*Corresponding author. Tel: +39 010 71781 725; E‐mail: davide.depietri{at}iit.it
DGCR8 and DICER are required for canonical miRNA biogenesis. This study describes miRNA‐independent roles of DGCR8 that control progenitor cell expansion and neurogenesis, and promote targeting of the mRNA of the cortical transcription factor Tbr1.
Synopsis
DGCR8 and DICER are required for canonical miRNA biogenesis. This study describes miRNA‐independent roles of DGCR8 that control progenitor cell expansion and neurogenesis, and promote targeting of the mRNA of the cortical transcription factor Tbr1.
Dgcr8 loss induces more severe cortical alterations as Dicer depletion, premature differentiation of basal progenitors, and the overproduction of TBR1+ neurons.
Depletion of miRNAs upon DCGR8 loss is reduced compared to DICER deficiency, revealing novel non‐canonical miRNAs in corticogenesis.
DGCR8 controls Tbr1 expression post‐transcriptionally and independently of miRNAs.
The DGCR8/DROSHA Microprocessor complex cleaves evolutionary conserved hairpins in the Tbr1 transcript.
EMBO Reports (2017) 18: 603–618
- Received May 27, 2016.
- Revision received January 16, 2017.
- Accepted January 19, 2017.
- © 2017 The Authors
- Nup358 binds to AGO proteins through its SUMO‐interacting motifs and promotes the association of target mRNA with miRISC
- Manas Ranjan Sahoo1,†,
- Swati Gaikwad1,†,
- Deepak Khuperkar1,
- Maitreyi Ashok1,
- Mary Helen1,
- Santosh Kumar Yadav1,
- Aditi Singh1,
- Indrasen Magre1,
- Prachi Deshmukh1,
- Supriya Dhanvijay1,
- Pabitra Kumar Sahoo1,
- Yogendra Ramtirtha2,
- Mallur Srivatsan Madhusudhan2,
- Pananghat Gayathri2,
- Vasudevan Seshadri1 and
- Jomon Joseph (josephj{at}nccs.res.in)*,1
- 1National Centre for Cell Science, S.P. Pune University Campus, Pune, India
- 2Division of Biology, Indian Institute of Science Education and Research, Pune, India
- ↵*Corresponding author. Tel: +91 20 25708084; E‐mail: josephj{at}nccs.res.in
↵† These authors contributed equally to this work
The nucleoporin Nup358 promotes the association of target mRNA with miRISC possibly at specialized ER domains and at the nuclear envelope. The study also identifies SIM as a new interacting motif for AGO family proteins.
Synopsis
The nucleoporin Nup358 promotes the association of target mRNA with miRISC possibly at specialized ER domains and at the nuclear envelope. The study also identifies SIM as a new interacting motif for AGO family proteins.
Nup358 depletion disrupts P body formation and impairs the coupling of target mRNA with miRISC.
Nup358 interacts with AGO proteins through its SUMO‐interacting motifs (SIMs), and SIM is identified as a new binding motif for AGO family proteins.
The association of target mRNA with miRISC possibly occurs at Nup358‐positive structures on the ER called annulate lamellae and at the nuclear envelope.
EMBO Reports (2017) 18: 241–263
- Received March 15, 2016.
- Revision received November 13, 2016.
- Accepted November 24, 2016.
- © 2016 The Authors
- A pseudouridine synthase module is essential for mitochondrial protein synthesis and cell viability
- Hana Antonicka1,
- Karine Choquet1,
- Zhen‐Yuan Lin2,
- Anne‐Claude Gingras2,3,
- Claudia L Kleinman4 and
- Eric A Shoubridge (eric{at}ericpc.mni.mcgill.ca)*,1
- 1Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
- 2Lunenfeld‐Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- 3Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- 4Department of Human Genetics, Segal Cancer Centre and Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- ↵*Corresponding author. Tel: +1 514 398 1997; Fax: +1 514 398 1509; E‐mail: eric{at}ericpc.mni.mcgill.ca
Using a proximity biotinylation assay, the authors identify a pseudouridine synthase module in mitochondrial RNA granules that is essential for epigenetic modification of the mitochondrial transcriptome, ribosome biogenesis, and mitochondrial protein synthesis.
Synopsis
Using a proximity biotinylation assay, the authors identify a pseudouridine synthase module in mitochondrial RNA granules that is essential for epigenetic modification of the mitochondrial transcriptome, ribosome biogenesis, and mitochondrial protein synthesis.
Mitochondrial RNA granules contain a pseudouridine synthase module.
Pseudouridylation of 16S rRNA by RPUSD4 is essential for mitochondrial ribosome assembly.
Pseudouridylation of specific mitochondrial mRNAs by TRUB2/RPUSD3 is necessary for their translation.
Epitranscriptomic modification of mitochondrial RNA is thus essential for cell viability.
EMBO Reports (2017) 18: 28–38
- Received September 22, 2016.
- Revision received November 21, 2016.
- Accepted November 22, 2016.
- © 2016 The Authors
- Architecture of the yeast Elongator complex
- Maria I Dauden1,
- Jan Kosinski1,
- Olga Kolaj‐Robin2,3,4,
- Ambroise Desfosses1,7,
- Alessandro Ori1,8,
- Celine Faux2,3,4,9,
- Niklas A Hoffmann1,
- Osita F Onuma5,
- Karin D Breunig5,
- Martin Beck1,
- Carsten Sachse1,
- Bertrand Séraphin2,3,4,
- Sebastian Glatt (sebastian.glatt{at}uj.edu.pl)*,6 and
- Christoph W Müller (cmueller{at}embl.de)*,1
- 1European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- 2Université de Strasbourg, IGBMC, Illkirch, France
- 3CNRS, IGBMC UMR 7104, Illkirch, France
- 4Inserm, IGBMC U964, Illkirch, France
- 5Institute of Biology, Martin Luther University Halle‐Wittenberg, Halle (Saale), Germany
- 6Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- 7Present Address: School of Biological Sciences, University of Auckland, Auckland, New Zealand
- 8Present Address: Leibniz Institute on Aging‐Fritz Lipmann Institute, Jena, Germany
- 9Present Address: CRBM – CNRS UMR5237, Montpellier, France
- ↵*
Corresponding author. Tel: +48 12 664 6321; E‐mail: sebastian.glatt{at}uj.edu.pl
Corresponding author. Tel: +49 6221 387 8320; E‐mail: cmueller{at}embl.de
The conserved Elongator complex specifically modifies tRNAs. An integrative modelling approach using data from negative‐stain EM and crosslinking mass spectrometry is used to obtain an architectural model of the fully assembled Elongator complex.
Synopsis
The conserved Elongator complex specifically modifies tRNAs. An integrative modelling approach using data from negative‐stain EM and crosslinking mass spectrometry is used to obtain an architectural model of the fully assembled Elongator complex.
Elp456 assembles asymmetrically on the Elp123 sub‐complex to form holoElongator.
A dense network of interactions connects all six Elongator subunits.
The enzymatically active Elp3 subunits are located in the center of this network.
EMBO Reports (2017) 18: 264–279
- Received September 15, 2016.
- Revision received October 20, 2016.
- Accepted November 8, 2016.
- © 2016 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.
- Molecular architecture of the yeast Elongator complex reveals an unexpected asymmetric subunit arrangement
- Dheva T Setiaputra1,
- Derrick TH Cheng1,
- Shan Lu2,
- Jesse M Hansen1,
- Udit Dalwadi1,
- Cindy HY Lam1,
- Jeffrey L To1,
- Meng‐Qiu Dong2 and
- Calvin K Yip (calvin.yip{at}ubc.ca)*,1
- 1Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
- 2National Institute of Biological Sciences, Beijing, Beijing, China
- ↵*Corresponding author. Tel: +1 604 827 3976; E‐mail: calvin.yip{at}ubc.ca
The conserved Elongator complex specifically modifies tRNAs. Here, the molecular architecture and subunit organization of yeast holo‐Elongator are reported based on single‐particle EM and cross‐linking mass spectrometry.
Synopsis
The conserved Elongator complex specifically modifies tRNAs. Here, the molecular architecture and subunit organization of yeast holo‐Elongator are reported based on single‐particle EM and cross‐linking mass spectrometry.
Negative stain electron microscopy analysis revealed that yeast holo‐Elongator adopts an asymmetric, bilobal architecture with the heterohexameric Elp456 subcomplex binding to only one of two Elp123 wing‐shaped lobes.
Cross‐linking coupled to mass spectrometry analysis identified the network of interactions among Elongator subunits and showed that Elp1, Elp3, and Elp4 form the structural core.
Elongator is capable of incorporating a second copy of Elp456, and its stoichiometry might be controlled by the available pool of Elp456 in the cytoplasm.
EMBO Reports (2017) 18: 280–291
- Received April 13, 2016.
- Revision received October 18, 2016.
- Accepted October 25, 2016.
- © 2016 The Authors
- Pseudouridylation of 7SK snRNA promotes 7SK snRNP formation to suppress HIV‐1 transcription and escape from latency
- 1Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- 2Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- 3Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- ↵*Corresponding author. Tel: +1 510 643 1697; E‐mail: qzhou{at}berkeley.edu
↵† These authors contributed equally to this work
7SK snRNA function is regulated by pseudouridylation, which stabilizes P‐TEFb‐sequestering 7SK snRNP and suppresses the transcription of HIV‐1 and cellular genes.
Synopsis
The 7SK RNA is an abundant non‐coding nuclear RNA that is highly conserved in vertebrates. This study indicates that its function can be modulated by pseudouridylation, which in turn controls transcription of both HIV‐1 and cellular genes.
The vast majority of cellular 7SK snRNA is pseudouridylated on U250 by the predominant cellular pseudouridine synthase machinery, the DKC1–box H/ACA RNP.
Pseudouridylation of 7SK RNA promotes formation of the 7SK snRNP that sequesters the general transcription elongation factor P‐TEFb into the catalytically inactive form to suppress HIV‐1 transcription and escape from latency.
EMBO Reports (2016) 17: 1441–1451
- Received May 5, 2016.
- Revision received July 27, 2016.
- Accepted July 28, 2016.
- © 2016 The Authors
- A novel long intergenic noncoding RNA indispensable for the cleavage of mouse two‐cell embryos
- Jiaqiang Wang1,2,†,
- Xin Li1,2,†,
- Leyun Wang1,2,†,
- Jingyu Li1,†,
- Yanhua Zhao1,
- Gerelchimeg Bou1,
- Yufei Li2,
- Guanyi Jiao2,
- Xinghui Shen3,
- Renyue Wei1,
- Shichao Liu1,
- Bingteng Xie1,
- Lei Lei3,
- Wei Li2,
- Qi Zhou (qzhou{at}ioz.ac.cn)*,2 and
- Zhonghua Liu (liu086{at}yahoo.com)*,1
- 1College of Life Science, Northeast Agricultural University, Harbin, China
- 2State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- 3Department of Histology and Embryology, Harbin Medical University, Harbin, China
- ↵*
Corresponding author. Tel: +86 1064807299; E‐mail: qzhou{at}ioz.ac.cn
Corresponding author. Tel: +86 45155191729; E‐mail: liu086{at}yahoo.com
↵† These authors contributed equally to this work
The ERV‐associated lincRNA, LincGET, is essential for mouse embryonic development beyond the two‐cell stage. LincGET forms an RNA‐protein complex with hnRNP U, FUBP1, and ILF2, participating in transcription regulation and exon skipping splicing activities.
Synopsis
The ERV‐associated lincRNA, LincGET, is essential for mouse embryonic development beyond the two‐cell stage. LincGET forms an RNA‐protein complex with hnRNP U, FUBP1, and ILF2, participating in transcription regulation and exon skipping splicing activities.
LincGET is a nuclear lincRNA that is GLN‐, MERVL‐, and ERVK‐associated and is only expressed in two‐ to four‐cell mouse embryos.
LincGET depletion leads to developmental arrest at the late G2 phase of the two‐cell stage with MAPK signaling pathway inhibition and aberrant exon skipping splicing activity.
LincGET forms an RNA‐protein complex with hnRNP U, FUBP1, and ILF2.
EMBO Reports (2016) 17: 1452–1470
- Received January 19, 2016.
- Revision received July 4, 2016.
- Accepted July 7, 2016.
- © 2016 The Authors
- Reduced hnRNPA3 increases C9orf72 repeat RNA levels and dipeptide‐repeat protein deposition
- Kohji Mori*,1,11,
- Yoshihiro Nihei1,
- Thomas Arzberger2,3,4,
- Qihui Zhou2,
- Ian R Mackenzie5,
- Andreas Hermann6,7,
- Frank Hanisch8,9,
- German Consortium for Frontotemporal Lobar Degeneration†,
- Bavarian Brain Banking Alliance‡,
- Frits Kamp1,
- Brigitte Nuscher1,
- Denise Orozco2,
- Dieter Edbauer2,10 and
- Christian Haass*,1,2,10
- 1Biomedical Center (BMC), Ludwig‐Maximilians‐University Munich, Munich, Germany
- 2German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- 3Center for Neuopathology and Prion Research, Ludwig‐Maximilians‐University Munich, Munich, Germany
- 4Department of Psychiatry and Psychotherapy, Ludwig‐Maximilians‐University Munich, Munich, Germany
- 5Department of Pathology, University of British Columbia and Vancouver General Hospital, Vancouver, Canada
- 6Deptartment of Neurology and Center for Regenerative Therapies Dresden (CRTD), Technical University Dresden, Dresden, Germany
- 7German Center for Neurodegenerative Diseases (DZNE), Dresden, Germany
- 8Department of Neurology, Martin‐Luther‐University Halle‐Wittenberg, Halle (Saale), Germany
- 9Department of Neurology, Vivantes Humboldt‐Klinikum, Berlin, Germany
- 10Munich Cluster for System Neurology (SyNergy), Munich, Germany
- 11Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- ↵*
Corresponding author. Tel: +49 89 4400 46549; E‐mail: christian.haass{at}mail03.med.uni-muenchen.de
Corresponding author. Tel: +81 6 6879 3051; E‐mail: kmori{at}psy.med.osaka-u.ac.jp
FTLD/ALS‐associated repeat expansions in C9orf72 are translated into dipeptide repeat proteins. Reduction of repeat‐binding hnRNPA3 increases levels of the repeat RNA and enhances production of dipeptide repeat proteins and RNA foci.
Synopsis
FTLD/ALS‐associated repeat expansions in C9orf72 are translated into dipeptide repeat proteins. Reduction of repeat‐binding hnRNPA3 increases levels of the repeat RNA and enhances production of dipeptide repeat proteins and RNA foci.
Reduction of nuclear hnRNPA3 increases levels of the C9orf72 repeat RNA.
Reduction of nuclear hnRNPA3 increases RNA foci formation and enhances generation and deposition of dipeptide repeat proteins.
Reduced nuclear hnRNPA3 in the hippocampus of patients with extended C9orf72 repeats correlates with increased dipeptide repeat protein deposition.
EMBO Reports (2016) 17: 1314–1325
- Received November 10, 2015.
- Revision received May 18, 2016.
- Accepted June 30, 2016.
- © 2016 The Authors
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