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Bensidoun P, Zenklusen D# and Oeffinger M#. Differential affinity purification and mass spectrometry analysis of two nuclear pore complex isoforms in yeast S. cerevisiae. STAR protocols. STAR protocols 2023 4 (3), 102359. #co-corresponding authors

Bensidoun P, Reiter T, Montpetit B, Zenklusen D# and Oeffinger M#. Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pores in budding yeast . Molecular Cell 2022 82 (20), 3856-3871. e6. #co-corresponding authors

Zhao C, Biondic S, Vandal K, Björklund ÅK, Hagemann-Jensen M, Sommer TM, Canizo J, Clark S, Raymond P, Raymond P, Zenklusen D, Rivron N, Reik W, Petropoulos S. Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids. Genome Research 2022 Aug 10;32(9):1627-41.

Adivarahan S, Abeykoon A, Zenklusen D. Single-molecule imaging suggests compact and spliceosome dependent organization of long introns. BioRxiv 2021

Bensidoun P, Zenklusen D# and Oeffinger M#. Choosing the right exit: How functional nuclear pore heterogeneity drives selective and efficient mRNA export. WIRES RNA 2021 May 2;e1660. 

Jayabalan AK, Adivarahan S, Koppula A, Abraham R, Batish M, Zenklusen D, Griffin DE, Leung AKL. Stress granule formation, disassembly, and composition are regulated by alphavirus ADP-ribosylhydrolase activity. Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):e2021719118. doi: 10.1073/pnas.2021719118. 

Adivarahan S, Zenklusen D. Probing the Conformational State of mRNPs Using smFISH and SIM. Methods Mol Biol. 2021;2209:267-286. doi: 10.1007/978-1-0716-0935-4_17.

Adivarahan S and Zenklusen D. Lessons from (pre-) mRNA Imaging. The Biology of mRNA: Structure and Function,  Adv Exp Med Biol. 2019; 1203:247-284.

Lari A, Farzam F, Bensidoun P, Oeffinger M, Zenklusen D, Grunwald D, Montpetit B. Live-Cell Imaging of mRNP–NPC Interactions in Budding Yeast. Imaging Gene Expression, Methods Mol Biol 2019;1203:247-284.

Adivarahan S, Livingston N, Nicholson B, Rahman S, Wu B, Rissland O, Zenklusen D. Spatial organization of single mRNPs at different stages of the gene expression pathway. Molecular Cell. Published online November 8, 2018.

Lessard F, Igelmann S, Huot G, Le Calvé B, Montero B, St-Germain E, Mignacca L, Deschênes-Simard X, Moiseeva O, Zorca CE, Zenklusen D, Brakier-Gingras L, Bourdeau V and Ferbeyre G.Defective ribosome biogenesis in senescence reveals a novel checkpoint pathway to block cyclin dependent kinases. Nature Cell Biology. Jul;20(7):789-799

King BR, Mueller F, Samacoits A, Eisenhauer PL, Ziegler CM, Bruce AE, Zenklusen D, Zimmer C, Botten J.A model of cyclical infection and clearance during persistence of arenavirus in individual cells revealed by single-molecule fluorescence in situ hybridization (smFISH). Journal of Virology. 2018 Apr 11. pii: JVI.02241-17. link

Trcek T, Rahman S and Zenklusen D. Measuring mRNA decay in budding yeast using single molecule FISH. Methods in Molecular Biology. 2018;1720:35-54.

Scott DD, Trahan C, Zindy PJ, Aguilar LC, Delubac M, Adivarahan S, Wei KE, Zenklusen D and Oeffinger M. Nol12 is a multifunctional endonuclease at the nexus of RNA and DNA metabolism. Nucleic Acid Research. 2017 Dec 1;45(21):12509-12528. link

King BR, Kellner S, Eisenhauer PL, Bruce EA, Ziegler CM, Zenklusen D, Botten JW. Visualization of the lymphocytic choriomeningitis mammarenavirus (LCMV) genome reveals the early endosome as a possible site for genome replication and viral particle pre-assembly. Journal of General Virology. 2017, Sep 27. doi: 10.1099/jgv.0.000930. link

Rahman S, Zorca C, Traboulsi T, Noutahi E, Krause M, Mader S and Zenklusen D. Single-cell profiling reveals that eRNA accumulation at enhancer-promoter loops is not required to sustain transcription. Nucleic Acid Research 2017, Apr 7;45(6):3017-3030. link

Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell 016 Nov 17;167(5):1215-1228.e25 link

Bensidoun P, Raymond P, Oeffinger M, Zenklusen D. Imaging single mRNAs to study dynamics of mRNA export in the yeast Saccharomyces cerevisiae. Methods 2016 Jan 16;S1046-2023(16) link

Saroufim MA, Bensidoun P, Raymond P, Rahman S, Krause MR, Oeffinger M, Zenklusen D. The nuclear basket mediates perinuclear mRNA scanning in budding yeast. Journal of Cell Biology 2015 Dec 21;211(6):1131-40 link

Smith C, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D, Weis K, Grunwald D, Montpetit B. In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. Journal of Cell Biology 2015, Dec 21;211(6):1121-30 link

Hocine S, Vera M, Zenklusen D, Singer RH Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH. Sci Rep. 2015 May 28;5:9934. link

Zorca CE, Kim LK, Kim YJ, Krause MR, Zenklusen D, Spilianakis CG, and Flavell RA. Myosin VI regulates gene pairing and transcriptional pause release in T cells. PNAS 2015, published ahead of print March 13. link

Rahman S and Zenklusen D. Single-Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiae. Methods Mol Biol. 2013;1042:33-46. link

Castelnuovo M, Rahman S, Guffanti E, Infantino V, Stutz F and Zenklusen D. Bimodal expression of PHO84 is modulated by early termination of antisense transcription. Nat Struct Mol Biol. 2013 Jul;20(7):851-8. link

Messier, V, Zenklusen D, Mishnick S. A nutrient responsive pathway that determines M-phase timing through control of B cyclin mRNA stability. Cell. 2013 May 23;153(5):1080-93. link

Hocine S, Raymond P, Zenklusen D, Chao JA and Singer RH. Single-molecule analysis of gene expression using two-color RNA labeling in live yeast. Nature Methods 2013 Feb;10(2):119-21 link

Oeffinger M, Zenklusen D. To the pore and through the pore: A story of mRNA export kinetics. Biochim Biophys Acta. 2012 Jun;1819(6):494-506. PDF

Trcek T, Chao J, Larson DR, Park HY, Zenklusen D, Shenoy S, Singer RH. Single-mRNA counting using fluorescent in situ hybridization in budding yeast. Nature Protocols. 2011 Feb 2;(7), 408–419. PDF

Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH. Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene. Science. 2011 Apr 22;332(6028):475-478. Evaluated by the Faculty of 1000. PDF

Powrie EA, Zenklusen D, Singer RH. A nucleoporin, Nup60p affects the nuclear and cytoplasmic localization of ASH1 mRNA in S. cerevisiae. RNA. 2011 Jan;17(1):134-44. Evaluated by the Faculty of 1000. PDF

Daniel’s papers @ Albert Einstein College of Medicine

Gandhi S, Zenklusen D, Lionnet T, Singer RH. Transcription of functionally related constitutive genes is not coordinated. Nat Struct Mol Biol. 2011 Jan;18(1):27-34. PDF

Zenklusen D and Singer RH. Analyzing mRNA expression using single mRNA resolution fluorescent in situ hybridization. Methods Enzymol. 2010, 470:641-659. PDF

Sanford JS, Pettia A, Slavova N, Parsonsa L, Briehof R, Thibergea SY, Zenklusen D, Gandhi S, Larson D, Singer RH and Botstein D. Metabolic Cycling in Single Yeast Cells from Unsynchronized Steady-State Populations Limited on Glucose or Phosphate. Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6946-51. Evaluated by the Faculty of 1000. PDF

Larson D, Singer RH, Zenklusen D. A Single Molecule View of Gene Expression. Trends Cell Biol. 2009 Nov;19(11):630-7. PDF

Oeffinger M, Zenklusen D, Wei KE, Ferguson A, El Hage A, Tollervey D, Singer RH, Chait BT and Rout MP. Rrp17p is a eukaryotic exonuclease required for 5′ end processing of pre-60S ribosomal RNA. Mol Cell. 2009 Dec 11; 36 (5): 768-81. PDF

Darzacq X, Yao J, Larson D, Bosnac L, deTurris V, Ruda V, Lionnet T, Zenklusen D, Causse S, Tjian R, Singer RH (Janelia Farm Research Consortium on Imaging Transcription). Imaging Transcription in Living Cells. Annual review of biophysics. 2009;38:173-96. PDF

Zenklusen D, Larson DR, Singer RH. Single RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol. 2008 Dec;15(12):1263-71. Evaluated by the Faculty of 1000. PDF

Wells AL, Condeelis JS, Singer RH, Zenklusen D. Imaging Real-Time Gene Expression in Living Systems. Laboratory Manual for Single Molecule Studies. Cold Spring Harbor Laboratory Press. 2008. ISBN  978-087969775-4.

Dong S, Li C, Zenklusen D, Singer RH, Jacobson A, He F. YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNA. Mol Cell. 2007 Feb 23;25(4):559-73. PDF

Huttelmaier S, Zenklusen D, Lederer M, Dictenberg J, Lorenz M, Meng X, Bassell GJ, Condeelis J, Singer RH. Spatial regulation of beta-actin translation by Src-dependent phosphorylation of ZBP1. Nature. 2005;438(7067):512-515. Evaluated by the Faculty of 1000. PDF

Niessing D, Huttelmaier S, Zenklusen D, Singer RH, Burley SK. She2p is a novel RNA binding protein with a basic helical hairpin motif. Cell 2004;119(4):491-502. PDF

Gu W, Deng Y, Zenklusen D, Singer RH. A new yeast PUF family protein, Puf6p, represses ASH1 mRNA translation and is required for its localization. Genes Dev. 2004;18(12):1452-65. Evaluated by the Faculty of 1000. PDF

Darzacq X, Powrie E, Gu W, Singer RH, Zenklusen D. RNA asymmetric distribution and daughter/mother differentiation in yeast. Curr Opin Microbiol. 2003; 6(6):614-20. PDF

Daniel’s papers @ Université de Lausanne

Vinciguerra P, Iglesias N, Camblong J, Zenklusen D, Stutz F. Perinuclear Mlp proteins downregulate gene expression in response to a defect in mRNA export. EMBO J. 2005; 24(4):813-23. PDF

Zenklusen D, Vinciguerra P, Wyss J-C, Stutz F. Stable mRNP formation and export requires co-transcriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol Cell Biol. 2002;22(23):8241-53. PDF

Hammell C.M, Gross S, Zenklusen D, Heath C.V, Stutz F, Moore C, Cole CN. Coupling of termination, 3′ processing and mRNA export. Mol Cell Biol. 2002;22(18):6441-57. PDF

Zenklusen D, Stutz F. Nuclear export of mRNA. FEBS Lett. 2001; 498(2-3):150-6. PDF

Zenklusen D, Vinciguerra P, Strahm Y, Stutz F. The yeast hnRNP-Like proteins Yra1p and Yra2p participate in mRNA export through interaction with Mex67p. Mol Cell Biol 2001; 21(13):4219-32. PDF

Strahm Y, Fahrenkrog B, Zenklusen D, Rychner E, Kantor J, Rosbach M, Stutz F. The RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr255p. EMBO J. 1999; 18(20):5761-77. PDF

Daniel’s papers @ Universität Bern

Martin F, Michel F, Zenklusen D, Muller B, Schumperli D. Positive and negative mutant selection in the human histone hairpin-binding protein using the yeast three-hybrid system. Nucleic Acids Res. 2000; 28(7):1594-603. PDF