RNA Society Newsletter August 2015
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The Ribosome As a Regulator of Mrna Decay
www.nature.com/cr www.cell-research.com RESEARCH HIGHLIGHT Make or break: the ribosome as a regulator of mRNA decay Anthony J. Veltri1, Karole N. D’Orazio1 and Rachel Green 1 Cell Research (2020) 30:195–196; https://doi.org/10.1038/s41422-019-0271-3 Cells regulate α- and β-tubulin levels through a negative present. To address this, the authors mixed pre-formed feedback loop which degrades tubulin mRNA upon detection TTC5–tubulin RNCs containing crosslinker with lysates from of excess free tubulin protein. In a recent study in Science, Lin colchicine-treated or colchicine-untreated TTC5-knockout cells et al. discover a role for a novel factor, TTC5, in recognizing (either having or lacking abundant free tubulin, respectively). the N-terminal motif of tubulins as they emerge from the After irradiation, TTC5 only crosslinked to the RNC in lysates ribosome and in signaling co-translational mRNA decay. from cells that had previously been treated with colchicine; Cells use translation-coupled mRNA decay for both quality these data suggested to the authors that some other (unknown) control and general regulation of mRNA levels. A variety of known factor may prevent TTC5 from binding under conditions of low quality control pathways including Nonsense Mediated Decay free tubulin. (NMD), No-Go Decay (NGD), and Non-Stop Decay (NSD) specifi- What are likely possibilities for how such coupling between cally detect and degrade mRNAs encoding potentially toxic translation and mRNA decay might occur? One example to protein fragments or sequences which cause ribosomes to consider is that of mRNA surveillance where extensive studies in translate poorly or stall.1 More generally, canonical mRNA yeast have identified a large group of proteins that recognize degradation is broadly thought to be translation dependent, and resolve stalled RNCs found on problematic mRNAs and 1234567890();,: though the mechanisms that drive these events are not target those mRNAs for decay. -
Nobel Laureates Endorse Joe Biden
Nobel Laureates endorse Joe Biden 81 American Nobel Laureates in Physics, Chemistry, and Medicine have signed this letter to express their support for former Vice President Joe Biden in the 2020 election for President of the United States. At no time in our nation’s history has there been a greater need for our leaders to appreciate the value of science in formulating public policy. During his long record of public service, Joe Biden has consistently demonstrated his willingness to listen to experts, his understanding of the value of international collaboration in research, and his respect for the contribution that immigrants make to the intellectual life of our country. As American citizens and as scientists, we wholeheartedly endorse Joe Biden for President. Name Category Prize Year Peter Agre Chemistry 2003 Sidney Altman Chemistry 1989 Frances H. Arnold Chemistry 2018 Paul Berg Chemistry 1980 Thomas R. Cech Chemistry 1989 Martin Chalfie Chemistry 2008 Elias James Corey Chemistry 1990 Joachim Frank Chemistry 2017 Walter Gilbert Chemistry 1980 John B. Goodenough Chemistry 2019 Alan Heeger Chemistry 2000 Dudley R. Herschbach Chemistry 1986 Roald Hoffmann Chemistry 1981 Brian K. Kobilka Chemistry 2012 Roger D. Kornberg Chemistry 2006 Robert J. Lefkowitz Chemistry 2012 Roderick MacKinnon Chemistry 2003 Paul L. Modrich Chemistry 2015 William E. Moerner Chemistry 2014 Mario J. Molina Chemistry 1995 Richard R. Schrock Chemistry 2005 K. Barry Sharpless Chemistry 2001 Sir James Fraser Stoddart Chemistry 2016 M. Stanley Whittingham Chemistry 2019 James P. Allison Medicine 2018 Richard Axel Medicine 2004 David Baltimore Medicine 1975 J. Michael Bishop Medicine 1989 Elizabeth H. Blackburn Medicine 2009 Michael S. -
Ribosomes Slide on Lysine-Encoding Homopolymeric a Stretches
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Crossref RESEARCH ARTICLE elifesciences.org Ribosomes slide on lysine-encoding homopolymeric A stretches Kristin S Koutmou1, Anthony P Schuller1, Julie L Brunelle1,2, Aditya Radhakrishnan1, Sergej Djuranovic3, Rachel Green1,2* 1Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, United States; 2Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, United States; 3Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, United States Abstract Protein output from synonymous codons is thought to be equivalent if appropriate tRNAs are sufficiently abundant. Here we show that mRNAs encoding iterated lysine codons, AAA or AAG, differentially impact protein synthesis: insertion of iterated AAA codons into an ORF diminishes protein expression more than insertion of synonymous AAG codons. Kinetic studies in E. coli reveal that differential protein production results from pausing on consecutive AAA-lysines followed by ribosome sliding on homopolymeric A sequence. Translation in a cell-free expression system demonstrates that diminished output from AAA-codon-containing reporters results from premature translation termination on out of frame stop codons following ribosome sliding. In eukaryotes, these premature termination events target the mRNAs for Nonsense-Mediated-Decay (NMD). The finding that ribosomes slide on homopolymeric A sequences explains bioinformatic analyses indicating that consecutive AAA codons are under-represented in gene-coding sequences. Ribosome ‘sliding’ represents an unexpected type of ribosome movement possible during translation. DOI: 10.7554/eLife.05534.001 *For correspondence: ragreen@ Introduction jhmi.edu Messenger RNA (mRNA) transcripts can contain errors that result in the production of incorrect protein products. -
Fall 2016 Is Available in the Laboratory of Dr
RNA Society Newsletter Aug 2016 From the Desk of the President, Sarah Woodson Greetings to all! I always enjoy attending the annual meetings of the RNA Society, but this year’s meeting in Kyoto was a standout in my opinion. This marked the second time that the RNA meeting has been held in Kyoto as a joint meeting with the RNA Society of Japan. (The first time was in 2011). Particular thanks go to the local organizers Mikiko Siomi and Tom Suzuki who took care of many logistical details, and to all of the organizers, Mikiko, Tom, Utz Fischer, Wendy Gilbert, David Lilley and Erik Sontheimer, for putting together a truly exciting and stimulating scientific program. Of course, the real excitement in the annual RNA meetings comes from all of you who give the talks and present the posters. I always enjoy meeting old friends and colleagues, but the many new participants in this year’s meeting particularly encouraged me. (Continued on p2) In this issue : Desk of the President, Sarah Woodson 1 Highlights of RNA 2016 : Kyoto Japan 4 Annual Society Award Winners 4 Jr Scientist activities 9 Mentor Mentee Lunch 10 New initiatives 12 Desk of our CEO, James McSwiggen 15 New Volunteer Opportunities 16 Chair, Meetings Committee, Benoit Chabot 17 Desk of the Membership Chair, Kristian Baker 18 Thank you Volunteers! 20 Meeting Reports: RNA Sponsored Meetings 22 Upcoming Meetings of Interest 27 Employment 31 1 Although the graceful city of Kyoto and its cultural months. First, in May 2016, the RNA journal treasures beckoned from just beyond the convention instituted a uniform price for manuscript publication hall, the meeting itself held more than enough (see p 12) that simplifies the calculation of author excitement to keep ones attention! Both the quality fees and facilitates the use of color figures to and the “polish” of the scientific presentations were convey scientific information. -
Determinants of Exon 7 Splicing in the Spinal Muscular Atrophy Genes, SMN1 and SMN2 Luca Cartegni,*,† Michelle L
Determinants of Exon 7 Splicing in the Spinal Muscular Atrophy Genes, SMN1 and SMN2 Luca Cartegni,*,† Michelle L. Hastings,* John A. Calarco,‡ Elisa de Stanchina, and Adrian R. Krainer Cold Spring Harbor Laboratory, Cold Spring Harbor, NY Spinal muscular atrophy is a neurodegenerative disorder caused by the deletion or mutation of the survival-of- motor-neuron gene, SMN1. An SMN1 paralog, SMN2, differs by a CrT transition in exon 7 that causes substantial skipping of this exon, such that SMN2 expresses only low levels of functional protein. A better understanding of SMN splicing mechanisms should facilitate the development of drugs that increase survival motor neuron (SMN) protein levels by improving SMN2 exon 7 inclusion. In addition, exonic mutations that cause defective splicing give rise to many genetic diseases, and the SMN1/2 system is a useful paradigm for understanding exon-identity determinants and alternative-splicing mechanisms. Skipping of SMN2 exon 7 was previously attributed either to the loss of an SF2/ASF–dependent exonic splicing enhancer or to the creation of an hnRNP A/B–dependent exonic splicing silencer, as a result of the CrT transition. We report the extensive testing of the enhancer-loss and silencer- gain models by mutagenesis, RNA interference, overexpression, RNA splicing, and RNA-protein interaction ex- periments. Our results support the enhancer-loss model but also demonstrate that hnRNP A/B proteins antagonize SF2/ASF–dependent ESE activity and promote exon 7 skipping by a mechanism that is independent of the CrT transition and is, therefore, common to both SMN1 and SMN2. Our findings explain the basis of defective SMN2 splicing, illustrate the fine balance between positive and negative determinants of exon identity and alternative splicing, and underscore the importance of antagonistic splicing factors and exonic elements in a disease context. -
Date: To: September 22, 1 997 Mr Ian Johnston©
22-SEP-1997 16:36 NOBELSTIFTELSEN 4& 8 6603847 SID 01 NOBELSTIFTELSEN The Nobel Foundation TELEFAX Date: September 22, 1 997 To: Mr Ian Johnston© Company: Executive Office of the Secretary-General Fax no: 0091-2129633511 From: The Nobel Foundation Total number of pages: olO MESSAGE DearMrJohnstone, With reference to your fax and to our telephone conversation, I am enclosing the address list of all Nobel Prize laureates. Yours sincerely, Ingr BergstrSm Mailing address: Bos StU S-102 45 Stockholm. Sweden Strat itddrtSMi Suircfatan 14 Teleptelrtts: (-MB S) 663 » 20 Fsuc (*-«>!) «W Jg 47 22-SEP-1997 16:36 NOBELSTIFTELSEN 46 B S603847 SID 02 22-SEP-1997 16:35 NOBELSTIFTELSEN 46 8 6603847 SID 03 Professor Willis E, Lamb Jr Prof. Aleksandre M. Prokhorov Dr. Leo EsaJki 848 North Norris Avenue Russian Academy of Sciences University of Tsukuba TUCSON, AZ 857 19 Leninskii Prospect 14 Tsukuba USA MSOCOWV71 Ibaraki Ru s s I a 305 Japan 59* c>io Dr. Tsung Dao Lee Professor Hans A. Bethe Professor Antony Hewlsh Department of Physics Cornell University Cavendish Laboratory Columbia University ITHACA, NY 14853 University of Cambridge 538 West I20th Street USA CAMBRIDGE CB3 OHE NEW YORK, NY 10027 England USA S96 014 S ' Dr. Chen Ning Yang Professor Murray Gell-Mann ^ Professor Aage Bohr The Institute for Department of Physics Niels Bohr Institutet Theoretical Physics California Institute of Technology Blegdamsvej 17 State University of New York PASADENA, CA91125 DK-2100 KOPENHAMN 0 STONY BROOK, NY 11794 USA D anni ark USA 595 600 613 Professor Owen Chamberlain Professor Louis Neel ' Professor Ben Mottelson 6068 Margarldo Drive Membre de rinstitute Nordita OAKLAND, CA 946 IS 15 Rue Marcel-Allegot Blegdamsvej 17 USA F-92190 MEUDON-BELLEVUE DK-2100 KOPENHAMN 0 Frankrike D an m ar k 599 615 Professor Donald A. -
Polysome-Profiling in Small Tissue Samples
bioRxiv preprint doi: https://doi.org/10.1101/104596; this version posted February 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Polysome-profiling in small tissue samples Shuo Liang1,#, Hermano Bellato2,#, Julie Lorent1,#, Fernanda Lupinacci2, Vincent Van Hoef1, Laia Masvidal1,*, Glaucia Hajj2,* and Ola Larsson1,* 1. Department of Oncology-Pathology, Karolinska Institutet, Stockholm, 171 77, Sweden 2. International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil # Equally contributing authors * Correspondence: Laia Masvidal ([email protected]), Glaucia Hajj ([email protected]) and Ola Larsson ([email protected]) ABSTRACT Polysome-profiling is commonly used to study genome wide patterns of translational efficiency, i.e. the translatome. The standard approach for collecting efficiently translated polysome-associated RNA results in laborious extraction of RNA from a large volume spread across multiple fractions. This property makes polysome-profiling inconvenient for larger experimental designs or samples with low RNA amounts such as primary cells or frozen tissues. To address this we optimized a non-linear sucrose gradient which reproducibly enriches for mRNAs associated with >3 ribosomes in only one or two fractions, thereby reducing sample handling 5-10 fold. The technique can be applied to cells and frozen tissue samples from biobanks, and generates RNA with a quality reflecting the starting material. When coupled with smart-seq2, a single-cell RNA sequencing technique, translatomes from small tissue samples can be obtained. Translatomes acquired using optimized non-linear gradients are very similar to those obtained when applying linear gradients. -
Using Ribosome Profiling to Quantify Differences in Protein Expression
bioRxiv preprint doi: https://doi.org/10.1101/501478; this version posted December 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Using ribosome profiling to quantify differences in protein expression: 2 a case study in Saccharomyces cerevisiae oxidative stress conditions 3 4 5 William R. Blevins1,#, Teresa Tavella1,#, Simone G. Moro1, Bernat Blasco-Moreno2, 6 Adrià Closa-Mosquera2, Juana Díez2, Lucas B. Carey2, M. Mar Albà1,2,3,* 7 8 1Evolutionary Genomics Groups, Research Programme on Biomedical Informatics (GRIB), Hospital del 9 Mar Research Institute (IMIM), Barcelona, Spain 10 2Health and Experimental Sciences Department, Universitat Pompeu Fabra(UPF), Barcelona, Spain 11 3Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain. 12 #Shared first co-authorship 13 *To whom correspondence should be addressed. 14 Running title: differential gene translation 15 Keywords: differential gene expression, ribosome profiling, RNA-Seq, translation, oxidative stress 1 bioRxiv preprint doi: https://doi.org/10.1101/501478; this version posted December 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 16 Abstract 17 18 Cells respond to changes in the environment by modifying the concentration of specific 19 proteins. Paradoxically, the cellular response is usually examined by measuring variations 20 in transcript abundance by high throughput RNA sequencing (RNA-Seq), instead of 21 directly measuring protein concentrations. -
The Complex Life of the Complex Life Of
The Complex Life of mRNA EMBO|EMBL Symposium 5–8 October 2016 Heidelberg | Germany EMBL Advanced Training Centre KEYNOTE SPEAKERS Thomas Cech Patrick Cramer Jennifer Doudna University of Colorado Boulder, USA MPI for Biophysical Chemistry, Germany University of California, Berkley, USA ABSTRACT SUBMISSION DEADLINE CONFIRMED SPEAKERS 13 JULY 2016 Maria Barna Rachel Green Shona Murphy Stanford University, USA Johns Hopkins University Sir William Dunn School of Pathology, UK School of Medicine, USA REGISTRATION DEADLINE Simon Bullock Karla Neugebauer 24 AUGUST 2016 MRC Laboratory of Molecular Biology, UK Chuan He Yale University, USA The University of Chicago, USA Emmanuelle Charpentier Uwe Ohler MPI for Infection Biology, Germany Alan Hinnebusch Max Delbrueck Center, Berlin, Germany ORGANISERS NIH, USA Anne Ephrussi Jeffrey Chao Laura Ranum EMBL Heidelberg, Germany Friedrich Miescher Institute for Elisa Izaurralde University of Florida, USA Biomedical Research, Switzerland MPI for Developmental Biology, Germany Nahum Sonenberg Erin Schuman McGill University, Canada Elena Conti Jeff Kieft MPI for Brain Research, Germany MPI of Biochemistry, Germany University of Colorado, USA Joan Steitz Yukihide Tomari Yale University, USA Victoria D'Souza Iain MacRae The University of Tokyo, Japan Harvard University, USA The Scripps Research Institute, USA David Tollervey Jonathan Weissman Wellcome Trust Centre for Cell Biology, UK Caroline Dean James Manley University of California, John Innes Centre, UK Columbia University, USA San Francisco, USA Additional speakers will be Gideon Dreyfuss Christine Mayr Marat Yusupov selected from abstracts. Perelman School of Medicine at the Memorial Sloan Kettering Cancer Institute of Genetics and Molecular University of Pennsylvania, USA Center, USA and Cellular Biology (IGBMC), France CONTACT www.embo-embl-symposia.org [email protected]. -
Super-Resolution Ribosome Profiling Reveals Unannotated Translation Events in Arabidopsis
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis Polly Yingshan Hsua, Lorenzo Calviellob,c, Hsin-Yen Larry Wud,1, Fay-Wei Lia,e,f,1, Carl J. Rothfelse,f, Uwe Ohlerb,c, and Philip N. Benfeya,g,2 aDepartment of Biology, Duke University, Durham, NC 27708; bBerlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; cDepartment of Biology, Humboldt Universität zu Berlin, 10099 Berlin, Germany; dBioinformatics Research Center and Department of Statistics, North Carolina State University, Raleigh, NC 27695; eUniversity Herbarium, University of California, Berkeley, CA 94720; fDepartment of Integrative Biology, University of California, Berkeley, CA 94720; and gHoward Hughes Medical Institute, Duke University, Durham, NC 27708 Contributed by Philip N. Benfey, September 13, 2016 (sent for review June 30, 2016; reviewed by Pam J. Green and Albrecht G. von Arnim) Deep sequencing of ribosome footprints (ribosome profiling) maps and contaminants. Several metrics associated with translation have and quantifies mRNA translation. Because ribosomes decode mRNA been exploited (11), for example, the following: (i)ribosomesre- every 3 nt, the periodic property of ribosome footprints could be lease after encountering a stop codon (9), (ii) local enrichment of used to identify novel translated ORFs. However, due to the limited footprints within the predicted ORF (4, 13), (iii) ribosome footprint resolution of existing methods, the 3-nt periodicity is observed length distribution (7), and (iv) 3-nt periodicity displayed by trans- mostly in a global analysis, but not in individual transcripts. Here, we lating ribosomes (2, 6, 10, 14, 15). Among these features, some work report a protocol applied to Arabidopsis that maps over 90% of the well in distinguishing groups of coding vs. -
Dissertation
Regulation of gene silencing: From microRNA biogenesis to post-translational modifications of TNRC6 complexes DISSERTATION zur Erlangung des DOKTORGRADES DER NATURWISSENSCHAFTEN (Dr. rer. nat.) der Fakultät Biologie und Vorklinische Medizin der Universität Regensburg vorgelegt von Johannes Danner aus Eggenfelden im Jahr 2017 Das Promotionsgesuch wurde eingereicht am: 12.09.2017 Die Arbeit wurde angeleitet von: Prof. Dr. Gunter Meister Johannes Danner Summary ‘From microRNA biogenesis to post-translational modifications of TNRC6 complexes’ summarizes the two main projects, beginning with the influence of specific RNA binding proteins on miRNA biogenesis processes. The fate of the mature miRNA is determined by the incorporation into Argonaute proteins followed by a complex formation with TNRC6 proteins as core molecules of gene silencing complexes. miRNAs are transcribed as stem-loop structured primary transcripts (pri-miRNA) by Pol II. The further nuclear processing is carried out by the microprocessor complex containing the RNase III enzyme Drosha, which cleaves the pri-miRNA to precursor-miRNA (pre-miRNA). After Exportin-5 mediated transport of the pre-miRNA to the cytoplasm, the RNase III enzyme Dicer cleaves off the terminal loop resulting in a 21-24 nt long double-stranded RNA. One of the strands is incorporated in the RNA-induced silencing complex (RISC), where it directly interacts with a member of the Argonaute protein family. The miRNA guides the mature RISC complex to partially complementary target sites on mRNAs leading to gene silencing. During this process TNRC6 proteins interact with Argonaute and recruit additional factors to mediate translational repression and target mRNA destabilization through deadenylation and decapping leading to mRNA decay. -
Pseudophosphorylated Αb-Crystallin Is a Nuclear Chaperone Imported Into the Nucleus with Help of the SMN Complex
Pseudophosphorylated αB-Crystallin Is a Nuclear Chaperone Imported into the Nucleus with Help of the SMN Complex John den Engelsman1, Chantal van de Schootbrugge1, Jeongsik Yong2, Ger J. M. Pruijn1, Wilbert C. Boelens1* 1 Department of Biomolecular Chemistry, Institute for Molecules and Materials and Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands, 2 Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota, United States of America Abstract The human small heat shock protein αB-crystallin (HspB5) is a molecular chaperone which is mainly localized in the cytoplasm. A small fraction can also be found in nuclear speckles, of which the localization is mediated by successional phosphorylation at Ser-59 and Ser-45. αB-crystallin does not contain a canonical nuclear localization signal sequence and the mechanism by which αB-crystallin is imported into the nucleus is not known. Here we show that after heat shock pseudophosphorylated αB-crystallin mutant αB-STD, in which all three phosphorylatable serine residues (Ser-19, Ser-45 and Ser-59) were replaced by negatively charged aspartate residues, is released from the nuclear speckles. This allows αB-crystallin to chaperone proteins in the nucleoplasm, as shown by the ability of αB- STD to restore nuclear firefly luciferase activity after a heat shock. With the help of a yeast two-hybrid screen we found that αB-crystallin can interact with the C-terminal part of Gemin3 and confirmed this interaction by co- immunoprecipitation. Gemin3 is a component of the SMN complex, which is involved in the assembly and nuclear import of U-snRNPs.