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Original Research Articles

Poetz F, Lebedeva S, Schott J, Lindner D, Ohler U, Stoecklin G. Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation. Genome Biol 2022; 23:193.

Klein P, Kallenberger SM, Roth H, Roth K, Ly-Hartig TBN, Magg V, Aleš J, Talemi SR, Qiang Y, Wolf S, Oleksiuk O, Kurilov R, Di Ventura B, Bartenschlager R, Eils R, Rohr K, Hamprecht FA, Höfer T, Fackler OT, Stoecklin G, Ruggieri A. Temporal control of the integrated stress response by a stochastic molecular switch. Sci Adv 2022; 8:eabk2022.

Hoerth K, Eiermann N, Beneke J, Erfle H, Stoecklin G. Image-Based Screening for Stress Granule Regulators. Methods Mol Biol 2022; 2428:361-379.

Eiermann N, Stoecklin G, Jovanovic B. Mitochondrial Inhibition by Sodium Azide Induces Assembly of eIF2α Phosphorylation-Independent Stress Granules in Mammalian Cells. Int J Mol Sci 2022; 23:5600.

Hisaoka M, Schott J, Bortecen T, Lindner D, Krijgsveld J, Stoecklin G. Preferential translation of p53 target genes. RNA Biology 2022; 19:1, 19:437-52.

Richter F, Plehn JE, Bessler L, Hertler J, Jörg M, Cirzi C, Tuorto F, Friedland K, Helm M. RNA marker modifications reveal the necessity for rigorous preparation protocols to avoid artifacts in epitranscriptomic analysis. Nucleic Acids Res 2022; 50:4201-15.

Poetz F, Corbo J, Levdansky Y, Spiegelhalter A, Lindner D, Magg V, Lebedeva S, Schweiggert J, Schott J, Valkov E, Stoecklin G. RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation. Nat Commun 2021; 12:7175.

Navarro IC, Tuorto F, Jordan D, Legrand C, Price J, Braukmann F, Hendrick AG, Akay A, Kotter A, Helm M, Lyko F, Miska EA. Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans. EMBO J 2021; 40:e105496.

Cirzi C, Tuorto F. Analysis of Queuosine tRNA Modification Using APB Northern Blot Assay. Methods Mol Biol 2021; 2298:217-30.

Sönmez A, Mustafa R, Ryll ST, Tuorto F, Wacheul L, Ponti D, Litke C, Hering T, Kojer K, Koch J, Pitzer C, Kirsch J, Neueder A, Kreiner G, Lafontaine DLJ, Orth M, Liss B, Parlato R. Nucleolar stress controls mutant Huntington toxicity and monitors Huntington's disease progression. Cell Death Dis 2021; 12:1139.

Amine H, Ripin N, Sharma S, Stoecklin G, Allain FH, Séraphin B, Mauxion F. A conserved motif in human BTG1 and BTG2 proteins mediates interaction with the poly(A) binding protein PABPC1 to stimulate mRNA deadenylation. RNA Biol 2021; 18:2450-65.

Jovanovic B, Eiermann N, Talwar D, Boulougouri M, Dick TP, Stoecklin G. Thioredoxin 1 is required for stress granule assembly upon arsenite-induced oxidative stress. Food Chem Toxicol 2021; 156:112508. 

Schott J, Reitter S, Lindner D, Grosser J, Bruer M, Shenoy A, Geiger T, Mathes A, Dobreva G, Stoecklin G. Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density. Nat Methods 2021; 18:1068-74.

Jovanovic B, Schubert L, Poetz F, Stoecklin G. Tagging of RPS9 as a tool for ribosome purification and identification of ribosome-associated proteins. Arch Biol Sci 2021; 73:47-55.

Lafarga V, Sirozh O, Díaz-López I, Galarreta A, Hisaoka M, Zarzuela E, Boskovic J, Jovanovic B, Fernandez-Leiro R, Muñoz J, Stoecklin G, Ventoso I, Fernandez-Capetillo O. Widespread displacement of DNA- and RNA-binding factors underlies toxicity of arginine-rich cell-penetrating peptides. EMBO J 2021; 40:e10331.

Boumezbeur AH, Bruer M, Stoecklin G, Mack M. Rational engineering of transcriptional riboswitches leads to enhanced metabolite levels in Bacillus subtilis. Metab Eng 2020; 61:58-68.

Haneke K, Schott J, Lindner D, Kruse Hollensen A, Kroun Damgaard C, Mongis C, Knop M, Palm W, Ruggieri A, Stoecklin G. CDK1 couples proliferation with protein synthesis. J Cell Biol. 2020; 219:e201906147.

Lafarga V, Sung HM, Haneke K, Roessig L, Pauleau AL, Bruer M, Rodriguez-Acebes S, Lopez-Contreras A, Gruss O, Erhardt S, Mendez J, Fernandez-Capetillo O, Stoecklin G. TIAR marks nuclear G2/M transition granules and restricts CDK1 activity under replication stress. EMBO Rep 2019; e46224.

Polycarpou-Schwarz M, Groß M, Mestdagh P, Schott J, Grund SE, Hildenbrand C, Rom J, Aulmann S, Sinn HP, Vandesompele J, Diederichs S. The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation. Oncogene 2018; 37:4750-68.

Lafarga V, Tapia O, Sharma S, Bengoechea R, Stoecklin G, Lafarga M, Berciano MT. CBP-mediated SMN acetylation modulates Cajal body biogenesis and the cytoplasmic targeting of SMN. Cell Mol Life Sci 2018; 3:527-46.

Vindry C, Marnef A, Broomhead H, Twyffels L, Ozgur S, Stoecklin G, Llorian M, Smith CW, Mata J, Weil D, Standart N. Dual RNA Processing Roles of Pat1b via Cytoplasmic Lsm1-7 and Nuclear Lsm2-8 Complexes. Cell Rep 2017; 5:1187-1200.

Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T, Plass C. DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. Nat Genet 2017; 7:1052-60.

Roth H, Magg V, Uch F, Mutz P, Klein P, Haneke K, Lohmann V, Bartenschlager R, Fackler OT, Locker N, Stoecklin G, Ruggieri A. Flavivirus Infection Uncouples Translation Suppression from Cellular Stress Responses. MBio 2017; 8:e02150.

Sharma S, Poetz F, Bruer M, Ly-Hartig TBN, Schott J, Séraphin B, Stoecklin G. Acetylation-Dependent Control of Global Poly(A) RNA Degradation by CBP/p300 and HDAC1/2. Mol Cell 2016; 63:927-38.

Cherkasov V, Grousl T, Theer P, Vainshtein Y, Gläßer C, Mongis C, Kramer G, Stoecklin G, Knop M, Mogk A, Bukau, B. Systemic control of protein synthesis through sequestration of translation and ribosome biogenesis factors during severe heat stress. FEBS Lett 2015; 589:3654-64.

Tuorto F, Herbst F, Alerasool N, Bender S, Pop O, Federico G, Reitter S, Liebers R, Stoecklin G, Gröne HJ, Dittmar G, Glimm H, Lyko F. The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during heamatopoiesis. EMBO J 2015; 34:2350-62.

Codutti L, Leppek K, Zálešák J, Windeisen V, Masiewicz P, Stoecklin G, Carlomagno T. A distinct, sequence-induced conformation is required for recognition of the CDE RNA by Roquin. Structure 2015; 23:4244-56.

Fischer-Kešo R, Breuninger S, Hofmann S, Henn M, Röhrig T, Ströbel P, Stoecklin G, Hofmann I. Plakophilins 1 and 3 bind to FXR1 and thereby influence the mRNA stability of desmosomal proteins. Mol Cell Bio 2014; 34:4244-56.

Leppek K, Stoecklin G. An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins. Nucleic Acids Res 2014; 42:e13

Schott J, Reitter S, Philipp J, Haneke K, Schäfer H, Stoecklin G. Translational regulation of specific mRNAs controls feedback inhibition and survival during macrophage activation. PLoS Genet 2014; 10:e1004368.

Schleich S, Strassburger K, Janiesch PC, Koledachkina T, Miller KK, Haneke K, Cheng YS, Küchler K, Stoecklin G, Duncan KE, Teleman AA. DENR-MRT-1 promotes translation re-initiation downstream of uORFs to control tissue growth. Nature 2014; 512:208-12.

Hämmerle M, Gutschner T, Uckelmann H, Ozgur S, Fiskin E, Gross M, Skawran B, Geffers R, Longerich T, Breuhahn K, Schirmacher P, Stoecklin G, Diederichs S. Posttranscriptional destabilization of the liver-specific long noncoding RNA HULC by the IGF2 mRNA-binding protein 1 (IGF2BP1). Hepatology 2013; 58:1703-12.

Cherkasov V, Hofmann S, Druffel-Augustin S, Mogk A, Tyedmers J, Stoecklin G, Bukau B. Coordination of translational control and protein homeostasis during severe heat stress. Curr Biol 2013; 23:2452-62.

Leppek K, Schott J, Reitter S, Poetz F, Hammond MC, Stoecklin G. Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs. Cell 2013; 153:869-81.

Ozgur S, Stoecklin G. Role fo Rck-Pat1b binding in assembly of processing-bodies. RNA Biol 2013; 10:528-39.

Färber V, Erben E, Sharma S, Stoecklin G, Clayton C. Trypanosome CNOT10 is essential for the integrity of the NOT deadenylase complex and for degradation of many mRNAs. Nucleic Acids Res 2013; 41:1211-22.

Hofmann S, Cherkasova V, Bankhead P, Bukau B, Stoecklin G. Translation suppression promotes stress ganule formation and cell survival in response to cold shock. Mol Biol Cell 2012; 23:3786-3800.

Tuorto F, Liebers R, Musch T, Schaefer M, Hofmann S, Kellner S, Frye M, Helm M, Stoecklin G, Lyko F. RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nat Struct Mol Biol 2012; 19:900-5.

Ruggieri A, Dazert E, Metz P, Hofmann S, Bergeest JP, Mazur J, Bankhead P, Hiet MS, Kallis S, Alvisi G, Samuel CE, Lohmann V, Kaderali L, Rohr K, Frese M, Stoecklin G, Bartenschlager R. Dynamic oscillation of translation and stress granule fomation mark the cellular response to virus infection. Cell Host Microbe 2012; 12:71-85.

Helfer S, Schott J, Stoecklin G, Förstemann K. AU-rich element-mediated mRNA decay can occur independently of the miRNA machinery in mouse embryonic fibroblasts and Drosophila S2-cells. PloS One 2012; 7:e28907.

Spasic M, Friedel CC, Schott J, Kreth J, Leppek K, Hofmann S, Ozgur S, Stoecklin G. Genome-wie assessment of AU-rich elements by the AREScore algorithm. PLoS Genet 2012; 8:e1002433.

Clement SL, Scheckel C, Stoecklin G, Lykke-Andersen J. Phosphorylation of tristetraprolin by MK2 impairs AU-rich element mRNA decay by preventing deadenylase recruitment. Mol Cell Biol 2011; 31:256-66.

Sandler H, Kreth J, Timmers HT, Stoecklin G. Not1 mediates recruitment of the deadenylase Caf1 to RNAs targeted for degradation by tristetraprolin. Nucleic Acids Res 2011; 39:4373-86.

Ozgur S, Chekulaeva M, Stoecklin G. Human Pat1b connects ceadenylation with RNA cecapping and controls the cssembly of processing bodies. Mol Cell Biol 2010; 30:4308-23.

Schwede A, Ellis L, Luther J, Carrington M, Stoecklin G, Clayton C. A role for Caf1 in mRNA deadenylation and decay in trypanosomes and human cells. Nucleic Acids Res 2008; 36:3374-88.

Stoecklin G, Tenenbaum SA, Mayo T, Chittur SV, George AD, Baroni TE, Blackshear PJ, Anderson P. Genome-wide analysis identifies interleukin-10 mRNA as target of tristetraprolin. J Biol Chem 2008; 283:11689-99.

Yamasaki S, Stoecklin G, Kedersha N, Simarro M, Anderson P. T-cell intracellular antigen-1 (TIA-1)-induced translation silencing promotes the decay of selected mRNAs. J Biol Chem 2007; 282:30070-7.

Sun L, Stoecklin G, Van Way S, Hinkovska-Galcheva V, Guo RF, Anderson P, Shanley TP. TTP/14-3-3 complex formation protects TTP from dephosphorylation by protein phosphatase 2A and stabilizes TNF-alpha mRNA. J Biol Chem 2007; 282:3766-77.

Benjamin D, Colombi M, Stoecklin G, Moroni C. A GFP-based assay for monitoring post-transcriptional regulation of ARE-mRNA turnover. Mol Biosyst 2006; 2:561-7.

Stoecklin G, Mayo T, Anderson P. ARE-mRNA degradation requires the 5'-3' decay pathway. EMBO Rep 2006; 7:72-7.

Kedersha N, Stoecklin G, Ayodele M, Yacono P, Lykke-Andersen J, Fritzler MJ, Scheuner D, Kaufman RJ, Golan DE, Anderson P. Stress granules and Processing Bodies are dynamically linked sites of mRNP remodeling. J Cell Biol 2005; 169:871-84.

Schmidlin M, Lu M, Leuenberger SA, Stoecklin G, Mallaun M, Gross B, Gherzi R, Hess D, Hemmings BA, Moroni C. The ARE-dependent mRNA-destabilizing activity of BRF1 is regulated by protein kinase B. EMBO J 2004; 23:4760-69.

Gilks N, Kedersha N, Ayodele M, Shen L, Stoecklin G, Dember LM, Anderson P. Stress granule assembly is mediated by prion-like aggregation of TIA-1. Mol Biol Cell 2004; 15:5383-98.

Stoecklin G, Stubbs T, Kedersha N, Wax S, Rigby WFC, Blackwell TK, Anderson P. MK2-induced tristetraprolin:14-3-3 complexes prevent stress granule association and ARE-mRNA decay. EMBO J 2004; 23:1313-24.

Stoecklin G, Lu M, Rattenbacher B, Moroni C. A constitutive decay element promotes tumor necrosis factor alpha mRNA degradation via an AU-rich element-independent pathway. Mol Cell Biol 2003; 23:3506-15.

Stoecklin G, Gross B, Ming XF, Moroni C. A novel mechanism of tumor suppression by destabilizing AU-rich growth factor mRNA. Oncogene 2003; 22:3554-61.

Stoecklin G, Colombi M, Raineri I, Leuenberger S, Mallaun M, Schmidlin M, Gross B, Lu M, Kitamura T, Moroni C. Functional cloning of BRF1, a regulator of ARE-dependent mRNA turnover. EMBO J 2002; 21:4709-18.

Chen CY, Gherzi R, Ong S, Chan E, Raijmakers R, Pruijn GJM, Stoecklin G, Moroni C, Mann M, Karin M. AU-binding proteins recruit the exosome to degrade ARE-containing mRNAs. Cell 2001; 107:451-64.

Stoecklin G, Stoeckle P, Lu M, Muehlemann O, Moroni C. Cellular mutants define a common mRNA degradation pathway targeting cytokine AU-rich elements. RNA 2001; 7:1578-88.

Ming XF, Stoecklin G, Lu M, Looser R, Moroni C. Parallel and independent regulation of interleukin-3 mRNA turnover by phosphatidylinositol 3-kinase and p38 mitogen-activated protein kinase. Mol Cell Biol 2001; 21:5778-89.

Stoecklin G, Ming XF, Looser R, Moroni C. Somatic mRNA turnover mutants implicate tristetraprolin in the interleukin-3 mRNA degradation pathway. Mol Cell Biol 2000; 20:3753-63.

Stoecklin G, Hahn S, Moroni C. Functional hierarchy of AUUUA motifs in mediating rapid interleukin-3 mRNA decay. J Biol Chem 1994; 269:28591-7.

Review Articles

Eiermann N, Haneke K, Sun Z, Stoecklin G, Ruggieri A. Dance with the Devil: Stress Granules and Signaling in Antiviral Responses. Viruses 2020; 12(9):984.

Erhardt S, Stoecklin G. The heat's on: nuclear stress bodies signal intron retention. EMBO J 2020; 39(3):e104154.

Ruggieri A, Stoecklin G. A signal to condense. Nat Chem Biol 2019; 15(1):5-6.

Stoecklin G and Bukau B. Telling right from wrong in life - cellular quality control. Nat Rev Mol Cell Biol 2013;14:613-5.

Stoecklin G and Mühlemann O. RNA decay mechanisms: Specificity through diversity. Biochim Biophys Acta 2013, 1829(6-7):487-90.

Stoecklin G and Kedersha N. Relationship of GW/P-bodies with stress granules. Adv Exp Med Biol 2013;768;197-211.

Leppek K, Schott J, Stoecklin G. Protein synthesis and translational control: at eye level with the ribosome. EMBO Rep 2011;12(12):1214-6.

Schott J, Stoecklin G. Networks controlling mRNA decay in the immune system. Wiley Interdiscip Rev RNA 2010;1:432-56.

Kulkarni M, Ozgur S, Stoecklin G. On track with P-bodies. Biochem Soc Trans 2010;38:242-51.

Sandler H, Stoecklin G. Control of mRNA decay by phosphorylation of tristetraprolin. Biochem Soc Trans 2008;36:491-6.

Stoecklin G, Anderson P. In a tight spot: ARE-mRNAs at processing bodies. Genes & Dev 2007;21:627-31.

Stoecklin G, Anderson P. Post-transcriptional mechanism regulating the inflammatory response. Adv Immunol 2006;89:1-37.

Newbury S, Muehlemann O and Stoecklin G. Turnover in the Alps: an mRNA perspective. EMBO Rep 2006;7:143-8.

Anderson P, Phillips K, Stoecklin G, Kedersha N. Posttranscriptional regulation of pro-inflammatory proteins. J Leuk Biol 2004;76:42-47.