@ IRCM

47. 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 (2023) Accepted (STAR-PROTOCOLS-D-23-00066-R1).

46. Valach M, Benz C, Aguilar LC, Gahura O, Faktorová D, Zíková A, Oeffinger M, Burger G, Gray MW, Lukeš J.  The diminutive mitoribosomal RNAs of diplonemid protists reside in a massive and complex protein shell. Nucl. Acid Res. (2023) May 19; gkad422. https://doi.org/10.1093/nar/gkad422

45. Trahan C and Oeffinger M. The Importance of being RNA-est: considering RNA-mediated ribosome plasticity. RNA Biology – Special Topic Issue: The Ribosome Life cycle. Review. (2023) Jan; 20(1):177-185. https://doi.org/10.1080/15476286.2023.2204581 

44. González L, Kolbin D, Trahan C, Jeronimo C, Robert F, Oeffinger M, Bloom K, and Michnick S. Transition from repressed to active chromatin drives partitioning of the INO1 locus to the nuclear periphery. Nature Comm. (2023) Feb 28;14(1):1135. doi: 10.1038/s41467-023-36391-6 PubMed

43. Bensidoun P, Reiter T, Montpetit B, Zenklusen D† and Oeffinger M†. Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast. Mol Cell (2022) Oct 20; 82. EPub Oct 10. https://doi.org/10.1016/j.molcel.2022.09.019 Mol Cell

42. Trahan C and Oeffinger M. Targeted cross-linking mass spectrometry on Single-Step Affinity Purified Molecular Complexes in the Yeast Saccharomyces cerevisiae. Methods in Mol Biol – Proteomics in Systems Biology: Methods and Protocols. Geddes-McAlister, J. (ed.); (2022) 2456:185-210. doi: 10.1007/978-1-0716-2124-0_13. PubMed

41. Trahan C and Oeffinger M. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae. Methods in Mol Biol – Yeast Functional Genomics-2^nd Edition. Devaux, F. (ed.); (2022) June 2477:195-223. doi: 10.1007/978-1-0716-2257-5_12. PubMed

40. Seffouh A, Trahan C, Wasi T, Jain N, Basu K, Britton RA, Oeffinger M, Ortega J. RbgA ensures the correct timing in the maturation of the 50S subunits functional sites. Nucl. Acid Res. (2022) Feb 10; doi: 10.1093/nar/gkac059. Breakthrough Article. Online ahead of print. PubMed

39. Osborne MJ, Volpon L, Memarpooryazdi M, Pillay S, Thambipillai A, Czarnota S, Culjkovic-Kraljacic B, Trahan C, Oeffinger M, Cowling VH, Borden KLB. Identification and characterization of the interaction between the methyl-7-guanosine cap maturation enzyme RNMT and the cap-binding protein eIF4E. J Mol Biology (2022) Jan 10;434(5):167451. doi: 10.1016/j.jmb.2022.167451 PubMed

38. Bensidoun P, Reiter T, Raymond P, Montpetit B, Zenklusen D† and Oeffinger M†. Nuclear mRNA metabolism directs specialization of the nuclear pore complex in yeast. †co-corresponding authors. bioRxiv (2021) doi: https://doi.org/10.1101/2021.11.07.467636

37. Helness A, Fraszczak J, Joly-Beauparlant C, Bagci H, Trahan C, Arman K, Shooshtarizadeh P, Chen R, Ayoub M, Côté JF, Oeffinger M, Droit A, and Möröy T. GFI1 tethers the nucleosome-remodeling and histone-deacetylase (NuRD) complex to open and transcriptionally active chromatin in myeloid progenitors. Commun. Biol. (2021) Dec 2;4 (1):1356. PubMed

36. Bensidoun P, Zenklusen D† and  Oeffinger M†. Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export. †co-corresponding authors. WIREs RNA. (2021) Nov; 12(6): e1660. EPub May 2. Review. PubMed

35. Knüppel R , Trahan C, Kern M, Wagner A, Grünberger F, Hausner W, Quax TEF, Albers S-V, Oeffinger M, and Ferreira-Cerca S. Insights into synthesis and function of KsgA/Dim1-dependent rRNA modifications in archaea. Nucl. Acid Res. (2021) Feb 22; 49(3):1662–1687. EPub Jan 12. https://doi.org/10.1093/nar/gkaa1268 PubMed Article

34. Aguilar LC*, Biplab P*, Gendron L, Nambi Rajan AA, Montpetit R, Trahan C, Pechmann S, Oeffinger M†, and Montpetit B†. Altered rRNA processing disrupts nuclear RNA homeostasis via competition for the poly(A)-binding protein Nab2. *co-first authors, †co-corresponding authors. Nucl. Acid Res. (2020) Nov 18;48(20):11675-11694. EPub Nov 2. Article 

33. Oeffinger M and Zenklusen D (eds.). The Biology of mRNA: Structure and Function. Book Series Advances in Experimental Medicine and Biology. Cham, Switzerland: Springer. 2019. Springer Preview

32. Scott DD, Aguilar LC, Kramar M, Oeffinger M. It’s Not the Destination, It’s the Journey: Heterogeneity in mRNA Export Mechanisms. Adv Exp Med Biol. (2019) 1203:33-81. Review. PubMed

31. de Oliveira CL, Volpon L, Rahardjo AK, Osborne MJ, Culjkovic-Kraljacic B, Trahan C, Oeffinger M, Kwok BH, Borden KLB. Structural studies of the eIF4E-VPg complex reveal a direct competition for capped RNA: Implications for translation. PNAS (2019) Nov 26;116(48):24056-24065. EPub Nov 11. PubMed PDF

30. Lari A*, Farzam F*, Bensidoun P,* Oeffinger M, Zenklusen D, Grunwald D, Montpetit B. Live-cell imaging of mRNP-NPC Interactions in Budding Yeast Methods Mol Biol (2019) 2038:138-150. PubMed

29. Lessard F, Igelmann S, Trahan C, Huot G, Saint-Germain E, Mignacca L, Del Toro N, Lopes-Paciencia S, Le Calvé B, Montero M, Deschênes-Simard X, Bury M, Moiseeva O, Rowell MC, Zorca CE, Zenklusen D, Brakier-Gingras L, Bourdeau V, Oeffinger M and Ferbeyre G. Senescence-associated ribosome biogenesis defects contribute to cell cycle arrest through the Rb pathway. Nat Cell Biology (2018) Jul;20(7):789-799. https://doi.org/10.1038/s41556-018-0127-y PubMed 

28. Scott DD, Trahan C, Aguilar LC, Delubac M, Adivarahan S, Van Nostrand E, Zindy PJ, Wei KE, Yeo G, Zenklusen D, and  Oeffinger M. Nol12 is a multifunctional RNA-binding protein at the nexus of RNA and DNA metabolism. Nucl. Acids Res. (2017) Dec 1;45(21):12509-12528. EPub Oct 23. https://doi.org/10.1093/nar/gkx963 PubMed PDF

27. Burlacu E, Lackmann F, Aguilar LC, van Nues R, Trahan C, Hector RD, Whiteley ND, Cockroft SL, Wieslander L, Oeffinger M, and Granneman S. High-throughput RNA structure probing reveals critical folding events during early stages of 60S ribosome biogenesis in yeast. Nature Comm. (2017) Sep 28;8(1):714. PubMed PDF

26. Vakiloroayaei A, Shah N, Oeffinger M, and Bayfield MA. The RNA chaperone La promotes pre-tRNA maturation via indiscriminate binding of both native and misfolded targets. Nucl. Acids Res. (2017) EPub Aug 31; https://doi.org/10.1093/nar/gkx764.  PubMed PDF

25. Milek M, Imami K, Mukherjee N, de Bortoli F, Zinnall U, Hazapis O, Trahan C, Oeffinger M, Heyd F, Ohler U, Selbach M, and Landthaler M. DDX54 regulates transcriptome dynamics during DNA damage response. Genome Research (2017) Aug;27(8):1344-1359. EPub June 8; PubMed PDF 

24. Reimer KA, Stark MA, Aguilar LC, Stark SR, Burke RD, Moore J, Fahlman RP, Yip CK, Kuroiwa H, Oeffinger M, and Rader SD. The sole LSm complex in Cyanidioschyzon merolae associates with pre-mRNA splicing and mRNA degradation factors. RNA (2017) June; 23: 952-967. EPub March 21; PubMed PDF 

23. Oeffinger M. Moulding the ribosome. Nature (2016) Sept 1; 537(7618):38-39. Nature PubMed 

22. Scott DD and Oeffinger M. Nucleolin and Nucleophosmin: nucleolar proteins with multiple functions in DNA repair. Biochem Cell Biol. (2016) Oct;94(5):419-432. Review. PubMed PDF

21. Scott DD, Trahan C, Zindy PJ, Aguilar LC, Delubac M, Wei KE, and Oeffinger M. Nol12 is a multifunctional endonuclease at the nexus of RNA and DNA metabolism. bioRxiv (2016) doi:http://dx.doi.org/10.1101/043935 bioRxiv PDF

20. Trahan C and Oeffinger M.  Targeted cross-linking-mass spectrometry determines vicinal interactomes within heterogeneous RNP complexes. Nucl. Acids Res. (2016) Feb; 44(3): 1354-69. EPub 2015 Dec 10. PubMed PDF 

19. Bensidoun P,  Raymond P, Oeffinger M, and Zenklusen D. Imaging single mRNAs to study dynamics of mRNA export in the Yeast S. cerevisiae. Methods (2016) Apr 1;98:104-14. Epub 2016 Jan 16. PubMed PDF

18. Trahan C, Aguilar LC and Oeffinger M. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae. Methods in Mol Biol – Yeast Functional Genomics (2016) Jan 1361: 265-87. PubMed  PDF

17. Saroufim MA, Bensidoun P, Raymond P,  Rahman S, Krause MR, Oeffinger M, and Zenklusen D.  The nuclear basket mediates perinuclear mRNA scanning in yeast.  J Cell Biol. (2015) Dec 21; 211 (6): 1131-40. PubMed  PDF

16. Oeffinger M and Montpetit B. Emerging properties of nuclear RNP biogenesis and export. Curr Opinion Cell Biol. – Special Issue Cell Nucleus (2015) June; (34): 46-53. Epub 2015 May 1. PubMed 

15. Fridy PC, Li Y, Keegan S, Thompson MK, Nudelman I, Scheid JF, Oeffinger M, Nussenzweig MC, Fenyö D, Chait BT, and Rout MP.  Rapid production of versatile nanobody repertoires. Nature Methods. (2014) Dec;11(12):1253-60. Epub 2014 Nov 2. PubMed 

14. Bretes H, Rouviere JO, Leger T, Oeffinger M, Devaux F, Doye V and Palancade B. Sumoylation of the THO complex regulates the biogenesis of a subset of mRNPs. Nucl. Acids Res. (2014) Feb; 43(2). Epub 2014 Feb 5. PubMed  PDF

13. Oeffinger M. Two Steps Forward – One Step Back: Advances in Affinity Purification Mass spectrometry of Macromolecular Complexes. Proteomics. (2012) May;12(10):1591-608. Review. PubMed  PDF

12. Oeffinger M and Zenklusen D. To The Pore and Through The Pore: A Story of mRNA Export Kinetics. Biochim Biophys Acta. (2012) June;1819(6):494-506. Review. PubMed  PDF

11. Oeffinger M. Joining the interface: a site for Nmd3 association on 60S subunits.     J Cell Biol. (2010) June 28; 189 (7): 1071-1073.  PubMed  PDF

@ Rockefeller University

10. Oeffinger M, Zenklusen D, Wei KE, Ferguson A, El Hage A, Tollervey D, Chait BT, Singer RH 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. PubMed PDF

9. Oeffinger M, Wei KE, Rogers R, DeGrasse JA, Chait BT, Aitchison JD and Rout MP. Comprehensive analysis of diverse ribonucleoprotein complexes. Nature Methods. (2007) Nov; 4(11): 951-6. Epub 2007 Oct 7. PubMed

8. Zhang J, HarnpicharnchaiP, Jakovljevic J, Tang L, Guo Y, Oeffinger M, Rout MP and Woolford JL, Jr. Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes Dev. (2007) Oct 15; 21(20): 2580-92. PubMed  PDF

7. Oeffinger M, Fatica A, Rout MP and Tollervey D. Yeast Rrp14p is required for ribosomal subunit synthesis and for correct positioning of the mitotic spindle during mitosis. Nucl. Acids Res. (2007) March 28; 35(4): 1354-1366. Epub 2007 Feb 1. PubMed PDF

6. Tackett AJ, DeGrasse JA, Sekedat MD, Oeffinger M, Rout MP, and Chait BT. I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J Proteome Res. (2005) Sep-Oct; 4(5): 1752-6. Epub 2005 Aug 25. PubMed

@ University of Edinburgh/Wellcome Trust Center

5. Oeffinger M, Dlakic M and Tollervey D. A pre-ribosome associated HEAT-repeat protein mediates export of both ribosomal subunits. Genes Dev. (2004) Jan 15; 18(2): 196-209. Epub 2004 Jan 16. PubMed  PDF

4. Oeffinger M and Tollervey D. The RNA-binding protein Nop15p is required for processing during 60S maturation and cell cycle progression. EMBO J. (2003) Dec 22; (24): 6573-83. PubMed PDF

3. Fatica A, Oeffinger M, Tollervey D and Bozzoni I. Cic1p/Nsa3p is required for synthesis and export of 60S ribosomal subunits. RNA (2003) Dec; 9(12): 1431-36. PubMed PDF

2. Fatica A, Oeffinger M, Dlakic M and Tollervey D. Nob1p is required for cleavage of the 3’end of the 18S rRNA. Mol Cell Biol. (2003) Mar; 23(5): 1798-807. PubMed  PDF

1. Oeffinger M, Leung A, Lamond A and Tollervey D. Yeast Pescadillo is required for multiple activities during 60S ribosomal subunit synthesis. RNA (2002) May; 8(5): 626-36. PubMed  PDF