Original Article Chronic Stress Reduces Spermatogenic Cell Proliferation in Rat Testis
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Extensive Translation of Circular Rnas Driven by N6-Methyladenosine
Cell Research (2017) 27:626-641. ORIGINAL ARTICLE www.nature.com/cr Extensive translation of circular RNAs driven by N6-methyladenosine Yun Yang1, 2, 3, 4, *, Xiaojuan Fan2, *, Miaowei Mao4, 5, *, Xiaowei Song2, 4, Ping Wu6, 7, Yang Zhang8, Yongfeng Jin1, Yi Yang5, Ling-Ling Chen8, Yang Wang9, Catherine CL Wong6, 7, Xinshu Xiao3, Zefeng Wang2, 4 1Institute of Biochemistry, College of Life Sciences, Zhejiang University at Zijingang, Zhejiang, Hangzhou, Zhejiang 310058, Chi- na; 2CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; 3Department of Integrative Biology and Physiology and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; 4Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; 5Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Sci- ence and Technology, Shanghai, China; 6National Center for Protein Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; 7Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China; 8Institute of Biochemistry and Cell Biology, Shanghai Institute for Biolog- ical Sciences, Chinese Academy of Sciences, Shanghai 200031, China; 9Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044, China Extensive pre-mRNA back-splicing generates numerous circular RNAs (circRNAs) in human transcriptome. However, the biological functions of these circRNAs remain largely unclear. Here we report that N6-methyladenosine (m6A), the most abundant base modification of RNA, promotes efficient initiation of protein translation from cir- cRNAs in human cells. -
Composition of Herpesvirus Ribonucleoprotein Complexes †
Abstract Composition of Herpesvirus Ribonucleoprotein Complexes † Eric S. Pringle 1,2,* and Craig McCormick 1,2 1 Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada; [email protected] 2 Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada * Correspondence: [email protected] † Presented at Viruses 2020—Novel Concepts in Virology, Barcelona, Spain, 5–7 February 2020. Published: 4 July 2020 Abstract: Herpesvirus genomes are decoded by host RNA polymerase enzymes, generating messenger ribonucleotides (mRNA) that are post-transcriptionally modified and exported to the cytoplasm through the combined work of host and viral factors. These viral mRNA bear 5′-m7GTP caps and poly(A) tails that should permit the assembly of canonical host eIF4F cap-binding complexes to initiate protein synthesis. However, the precise mechanisms of translation initiation remain to be investigated for Kaposi’s sarcoma-associated herpesvirus (KSHV) and other herpesviruses. During KSHV lytic replication in lymphoid cells, the activation of caspases leads to the cleavage of eIF4G and depletion of eIF4F. Translating mRNPs depleted of eIF4F retain viral mRNA, suggesting that non-eIF4F translation initiation is sufficient to support viral protein synthesis. To identify proteins required to support viral protein synthesis, we isolated and characterized actively translating messenger ribonucleoprotein (mRNP) complexes by ultracentrifugation and sucrose-gradient fractionation followed by quantitative mass spectrometry. The abundance of host translation initiation factors available to initiate viral protein synthesis were comparable between cells undergoing KSHV lytic or latent replication. The translation initiation factors eIF4E2, NCBP1, eIF4G2, and eIF3d were detected in association with actively translating mRNP complexes during KSHV lytic replication, but their depletion by RNA silencing did not affect virion production. -
Structural Characterization of the Human Eukaryotic Initiation Factor 3 Protein Complex by Mass Spectrometry*□S
Supplemental Material can be found at: http://www.mcponline.org/cgi/content/full/M600399-MCP200 /DC1 Research Structural Characterization of the Human Eukaryotic Initiation Factor 3 Protein Complex by Mass Spectrometry*□S Eugen Damoc‡, Christopher S. Fraser§, Min Zhou¶, Hortense Videler¶, Greg L. Mayeurʈ, John W. B. Hersheyʈ, Jennifer A. Doudna§, Carol V. Robinson¶**, and Julie A. Leary‡ ‡‡ Protein synthesis in mammalian cells requires initiation The initiation phase of eukaryotic protein synthesis involves factor eIF3, an ϳ800-kDa protein complex that plays a formation of an 80 S ribosomal complex containing the initi- Downloaded from central role in binding of initiator methionyl-tRNA and ator methionyl-tRNAi bound to the initiation codon in the mRNA to the 40 S ribosomal subunit to form the 48 S mRNA. This is a multistep process promoted by proteins initiation complex. The eIF3 complex also prevents pre- called eukaryotic initiation factors (eIFs).1 Currently at least 12 mature association of the 40 and 60 S ribosomal subunits eIFs, composed of at least 29 distinct subunits, have been and interacts with other initiation factors involved in start identified (1). Mammalian eIF3, the largest initiation factor, is a codon selection. The molecular mechanisms by which multisubunit complex with an apparent molecular mass of www.mcponline.org eIF3 exerts these functions are poorly understood. Since ϳ800 kDa. This protein complex plays an essential role in its initial characterization in the 1970s, the exact size, translation by binding directly to the 40 S ribosomal subunit composition, and post-translational modifications of and promoting formation of the 43 S preinitiation complex ⅐ ⅐ mammalian eIF3 have not been rigorously determined. -
Human Germ/Stem Cell-Specific Gene TEX19 Influences Cancer Cell
Planells-Palop et al. Molecular Cancer (2017) 16:84 DOI 10.1186/s12943-017-0653-4 RESEARCH Open Access Human germ/stem cell-specific gene TEX19 influences cancer cell proliferation and cancer prognosis Vicente Planells-Palop1, Ali Hazazi1, Julia Feichtinger2,3, Jana Jezkova1, Gerhard Thallinger2,3, Naif O. Alsiwiehri1, Mikhlid Almutairi1,5, Lee Parry4, Jane A. Wakeman1 and Ramsay J. McFarlane1* Abstract Background: Cancer/testis (CT) genes have expression normally restricted to the testis, but become activated during oncogenesis, so they have excellent potential as cancer-specific biomarkers. Evidence is starting to emerge to indicate that they also provide function(s) in the oncogenic programme. Human TEX19 is a recently identified CT gene, but a functional role for TEX19 in cancer has not yet been defined. Methods: siRNA was used to deplete TEX19 levels in various cancer cell lines. This was extended using shRNA to deplete TEX19 in vivo. Western blotting, fluorescence activated cell sorting and immunofluorescence were used to study the effect of TEX19 depletion in cancer cells and to localize TEX19 in normal testis and cancer cells/tissues. RT-qPCR and RNA sequencing were employed to determine the changes to the transcriptome of cancer cells depleted for TEX19 and Kaplan-Meier plots were generated to explore the relationship between TEX19 expression and prognosis for a range of cancer types. Results: Depletion of TEX19 levels in a range of cancer cell lines in vitro and in vivo restricts cellular proliferation/ self-renewal/reduces tumour volume, indicating TEX19 is required for cancer cell proliferative/self-renewal potential. Analysis of cells depleted for TEX19 indicates they enter a quiescent-like state and have subtle defects in S-phase progression. -
EIF4G2 Rabbit Pab
Leader in Biomolecular Solutions for Life Science EIF4G2 Rabbit pAb Catalog No.: A2897 Basic Information Background Catalog No. Translation initiation is mediated by specific recognition of the cap structure by A2897 eukaryotic translation initiation factor 4F (eIF4F), which is a cap binding protein complex that consists of three subunits: eIF4A, eIF4E and eIF4G. The protein encoded by this gene Observed MW shares similarity with the C-terminal region of eIF4G that contains the binding sites for 102kDa eIF4A and eIF3; eIF4G, in addition, contains a binding site for eIF4E at the N-terminus. Unlike eIF4G, which supports cap-dependent and independent translation, this gene Calculated MW product functions as a general repressor of translation by forming translationally 98kDa/102kDa inactive complexes. In vitro and in vivo studies indicate that translation of this mRNA initiates exclusively at a non-AUG (GUG) codon. Alternatively spliced transcript variants Category encoding different isoforms of this gene have been described. Primary antibody Applications WB, IHC, IF, IP Cross-Reactivity Human, Mouse, Rat Recommended Dilutions Immunogen Information WB 1:500 - 1:1000 Gene ID Swiss Prot 1982 P78344 IHC 1:100 - 1:200 Immunogen 1:50 - 1:200 IF A synthetic peptide corresponding to a sequence within amino acids 750-850 of human EIF4G2 (NP_001409.3). IP 1:50 - 1:200 Synonyms EIF4G2;AAG1;DAP5;NAT1;P97 Contact Product Information www.abclonal.com Source Isotype Purification Rabbit IgG Affinity purification Storage Store at -20℃. Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide,50% glycerol,pH7.3. Validation Data Western blot analysis of extracts of various cell lines, using EIF4G2 antibody (A2897) at 1:400 dilution. -
Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491 -
Robust Heat Shock Induces Eif2α-Phosphorylation
2078 Research Article Robust heat shock induces eIF2α-phosphorylation- independent assembly of stress granules containing eIF3 and 40S ribosomal subunits in budding yeast, Saccharomyces cerevisiae Tomás Grousl1, Pavel Ivanov1,*, Ivana Frydlová1, Pavla Vasicová1, Filip Janda1, Jana Vojtová1, Katerina Malínská1, Ivana Malcová1, Lenka Nováková1, Dana Janosková1, Leos Valásek2 and Jirí Hasek1,‡ 1Laboratory of Cell Reproduction, Institute of Microbiology of the AS CR, v.v.i., Prague, Czech Republic 2Laboratory of Regulation of Gene Expression, Institute of Microbiology of the AS CR, v.v.i., Prague, Czech Republic *Present address: A.N. Belozersky Institute of Physico-Chemical Biology MSU, Moscow, Russia ‡Author for correspondence (e-mail: [email protected]) Accepted 18 March 2009 Journal of Cell Science 122, 2078-2088 Published by The Company of Biologists 2009 doi:10.1242/jcs.045104 Summary Environmental stresses inducing translation arrest are markers also colocalized with eIF3a. Microscopic analyses of accompanied by the deposition of translational components into the edc3Δlsm4ΔC mutant demonstrated that different stress granules (SGs) serving as mRNA triage sites. It has scaffolding proteins are required to induce SGs upon robust recently been reported that, in Saccharomyces cerevisiae, heat shock as opposed to glucose deprivation. Even though formation of SGs occurs as a result of a prolonged glucose eIF2α became phosphorylated under these stress conditions, the starvation. However, these SGs did not contain eIF3, one of decrease in polysomes and formation of SGs occurred hallmarks of mammalian SGs. We have analyzed the effect of independently of phosphorylation of eIF2α. We conclude that robust heat shock on distribution of eIF3a/Tif32p/Rpg1p and under specific stress conditions, such as robust heat shock, yeast showed that it results in the formation of eIF3a accumulations SGs do contain eIF3 and 40S ribosomes and utilize alternative containing other eIF3 subunits, known yeast SG components routes for their assembly. -
CHARACTERIZING the INTERACTION BETWEEN PDCD4 and Eif3 with RESPECT to TRANSLATION REGULATION
CHARACTERIZING THE INTERACTION BETWEEN PDCD4 AND eIF3 WITH RESPECT TO TRANSLATION REGULATION DIVYA SHARMA KHANDIGA Master of Science, Bangalore University, India 2009 A Thesis/Project Submitted to the School of Graduate Studies of the University of Lethbridge in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE Department of Chemistry and Biochemistry University of Lethbridge LETHBRIDGE, ALBERTA, CANADA © Divya Sharma Khandiga, 2017 CHARACTERIZING THE INTERACTION BETWEEN PDCD4 AND eIF3 WITH RESPECT TO TRANSLATION REGULATION DIVYA SHARMA KHANDIGA Date of Defense: December 12, 2017 Dr. N. Thakor Assistant Professor Ph.D. Thesis Supervisor Dr. M. Roussel Professor Ph.D. Thesis Co-supervisor Dr. U. Kothe Associate Professor Ph.D. Thesis Examination Committee Member Dr. R. Golsteyn Associate Professor Ph.D. Thesis Examination Committee Member Dr. R. Fahlman Professor Ph.D. External Examiner University of Alberta Edmonton, Alberta Dr. M. Gerken Professor Ph.D. Chair, Thesis Examination Committee Dedication To my beloved family and friends, My inspiration, my parents Subraya Sharma and Kamala Sharma My dearly loved husband Samarth, sister Dr. Lakshmi and brother-in-law Dr. Pradeep My cute little niece Mithali and nephew Aathreya My adorable brother Dr. Ganesh, sister Dr. Sharadha, Silly Vidya and little angels My loving cousins and in-laws I am grateful to have them in my life, it is their well wishes, teachings, support and love that have enabled me to achieve success and happiness in life. iii Abstract Programmed cell death protein 4 (PDCD4) inhibits IRES-mediated translation of anti- apoptotic proteins such as XIAP. PDCD4 was shown to directly interact with the XIAP IRES element and inhibit translation initiation. -
Cellular and Molecular Signatures in the Disease Tissue of Early
Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of -
Genes with 5' Terminal Oligopyrimidine Tracts Preferentially Escape Global Suppression of Translation by the SARS-Cov-2 NSP1 Protein
Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein Shilpa Raoa, Ian Hoskinsa, Tori Tonna, P. Daniela Garciaa, Hakan Ozadama, Elif Sarinay Cenika, Can Cenika,1 a Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA 1Corresponding author: [email protected] Key words: SARS-CoV-2, Nsp1, MeTAFlow, translation, ribosome profiling, RNA-Seq, 5′ TOP, Ribo-Seq, gene expression 1 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover that a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5′ terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. -
Early Alterations of RNA Metabolism and Splicing from Adult Corticospinal Neurons In
bioRxiv preprint doi: https://doi.org/10.1101/667733; this version posted June 12, 2019. 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. 1 Early alterations of RNA metabolism and splicing from adult corticospinal neurons in 2 an ALS mouse model 3 4 Christine Marques1,2, Mathieu Fischer1,3, Céline Keime4, Thibaut Burg1, Aurore Brunet1, 5 Jelena Scekic-Zahirovic1 & Caroline Rouaux1* 6 7 8 9 1Inserm UMR_S 1118, Mécanismes centraux et périphériques de la neurodégénérescence, 10 Faculté de Médecine, Université de Strasbourg, Strasbourg, France. 11 2Current address: Department of Neurobiology, Harvard Medical School, Boston, MA, USA; 12 Department of Neurology, Massachusetts General Hospital, Boston, MA, USA. 13 3Current address: Department of Paediatrics, John Radcliffe Hospital, University of Oxford, 14 Oxford, UK. 15 4Inserm UMR_S 1258, CRNS UMR_S 7104, Université de Strasbourg, IGBMC, Strasbourg, 16 France. 17 18 *Correspondence should be addressed to: C.R. ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/667733; this version posted June 12, 2019. 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. Abstract Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease clinically defined as the combined degeneration of corticospinal and corticobulbar neurons (CSN), and bulbar and spinal motor neurons (MN). A growing body of evidence points to the motor cortex, where CSN are located, as the potential initiation site of ALS. However, little is known about the spatiotemporal dynamics of CSN degeneration and the molecular pathways involved. -
The Eif3 Complex of Typanosoma Brucei: Composition Conservation Does Not Imply the Conservation of Structural Assembly and Subunits Function
Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 1 The eIF3 complex of Typanosoma brucei: composition conservation does not imply the 2 conservation of structural assembly and subunits function 3 4 Kunrao Li,1,2 Shuru Zhou,1,2 Qixuan Guo,3 Xin Chen,1,2 Dehua Lai,2,4 Zhaorong Lun,2,4,5 and 5 Xuemin Guo1,2,5 6 7 1Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, 8 Guangzhou, China 9 2Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, 10 Guangzhou, China 11 3Chengde Nursing Vocational College, Chende, China 12 4Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, 13 Sun Yat-Sen University, Guangzhou, China 14 15 5Corresponding author. Email, [email protected]; or [email protected] 16 K.L. and S.Z. contributed equally to this work 17 18 Running head: Characterization of the eIF3 of Trypanosoma brucei 19 Keywords: Translation, Eukaryotic initiation factor 3, Trypanosome 20 1 Downloaded from rnajournal.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press 21 ABSTRACT 22 The multisubunit eukaryotic initiation factor 3 (eIF3) plays multiple roles in translation, but 23 poorly understood in trypanosomes. The putative subunits eIF3a and eIF3f of Trypanosoma 24 brucei (TbIF3a and TbIF3f) were overexpressed and purified, and 11 subunits were identified, 25 TbIF3a through l minus j, which form a tight complex. Both TbIF3a and TbIF3f are essential for 26 viability of T. brucei. RNAi knockdown of either of them severely reduced total translation and 27 the ratio of polysome/80S peak area.