Publications

2025

• Spangler, R.K.^#, Braun, K.^#, Ashley, G.E.^#, van der Does, M., Wruck, D., Ramos-Coronado, A., Ragle, J.M., Iesmantavicius, V., Morales Moya, L.J., Partch, C.L., Großhans, H.^*, Ward, J.D.^* A conserved chronobiological complex times C. elegans development. EMBO J. doi: https://doi.org/10.1038/s44318-025-00585-z (^# equal contribution) 
  News & Views: Hui & Ripperger, EMBO J 2025: https://doi.org/10.1038/s44318-025-00586-y
  
  
• Gaidatzis, D.^#, Graf-Landua, M.^#, Methot, S.P.^#, Wölk, M., Brancati, G., Hauser, Y.P., Meeuse, M.W.M., Nahar, S., Braun, K., van der Does, M., Aluri, S., Kohler, H., Smallwood, S., Großhans, H. (2025) A scheduler for rhythmic gene expression. Mol Syst Biol. doi: 10.1038/s44320-025-00155-9. (^# equal contribution)
  
  
• Harvey, L.M., Frédérick, P.M., Gudipati, R., Michaud, P., Houle, F., Young, D., Desbiens, C., Ladouceur, S., Dufour, A., Großhans, H., Simard, M. (2025). Dipeptidyl peptidase DPF-3 is a gatekeeper of microRNA Argonaute compensation in animals. Nat Commun 16: 2738

2024

• Nahar, S^#, Morales Moya, L.J. ^#, Brunner, J., Hendriks, G.-J., Towbin, B., Hauser, Y.P., Brancati, G., Gaidatzis, D.^*, Großhans, H.^* (2024) Dynamics of miRNA accumulation during C. elegans larval development. Nucleic Acids Res.52: 5336–5355 (^# equal contribution) 

• Gudipati, R.K.^#, Gaidatzis, D. ^#, Seebacher, S.,, Muehlhaeusser, S., Kempf, G., Cavadini, S., Hess, D, Soneson, C., and Großhans, H.^* (2024). Deep quantification of substrate turnover defines protease subsite cooperativity. Mol Syst Biol. 20: 1303 – 1328 (^# equal contribution) 

2023

• Welte, T.^*, Goulois, A., Stadler, M.B., Hess, D., Soneson, C., Neagu, A., Azzi, C., Lübke, M.J., Seebacher, J., Schmidt, I., Estoppey, D., Nigsch, F., Reece-Hoyes, J., Hoepfner, D, Großhans, H.^* (2023) Convergence of multiple RNA-silencing pathways on GW182/TNRC6. Mol Cell 83: 2478-2492.E8. https://doi.org/10.1101/gad.328492.119

• Meeuse, M.W.M., Hauser, Y.P., Nahar, S., Smith, A.A.T., Braun, K., Azzi, C., Rempfler, M., Großhans, H.^* (2023) The Grainyhead/LSF transcription factor GRH-1 is rhythmically required for molting. EMBO J. e111895. https://doi.org/10.15252/embj.2022111895

• Quévillon Huberdeau, M., Nilesh Shah, V., Nahar, S., Neumeier, J., Houle, F., Bruckmann, A., Gypas, F., Nakanishi, K., Großhans, H., Meister, G., and Simard, M.J.^* (2022) A specific Argonaute phosphorylation regulates the binding to microRNAs during C. elegans development. Cell Rep. 41: 111822. https://doi.org/10.1016/j.celrep.2022.111822

• Stojanovski, K., Großhans, H.^*, and Towbin, B.D.^* (2022) Coupling of growth rate and developmental tempo reduces body size heterogeneity in C. elegans. Nat Commun 13:3132. https://doi.org/10.1038/s41467-022-29720-8

• Methot, S.P.^#, Padeken, J.^#, Brancati, G., Zeller, P., Delaney, C.E., Gaidatzis, D., Kohler, H., van Oudenaarden, A., Großhans, H., and Gasser, S.M.^* (2021) H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity. Nat Cell Biol. 23:1163-1175. https://doi.org/10.1038/s41556-021-00776-w (^# equal contribution) 

• Tsiairis, C.^*, and Großhans, H.^* (2021) Gene expression oscillations in C. elegans underlie a new developmental clock. Curr Top Dev Biol. 2021;144:19-43. https://doi.org/10.1016/bs.ctdb.2020.11.001

• Gudipati, R.K.^*, Braun, K.^#, Gypas, F.^#, Hess, D., Schreier^, J.,Carl, S.H., Ketting, R.F., and Großhans, H.^* (2021) Protease-mediated processing of Argonaute proteins controls small RNA association. Mol Cell 81:2388-2402.e8. https://doi.org/10.1016/j.molcel.2021.03.029 (^# equal contribution) 

• Meeuse, M.W.M.^#, Hauser, Y.P.^#, Morales Moya, L.J., Hendriks, G.-J., Eglinger, J., Bogaarts, G., Tsiairis, C., and Großhans, H.^* (2020) Developmental function and state transitions of a gene expression oscillator in C. elegans. Mol Syst Biol. 16: e9498. https://doi.org/10.15252/msb.209975 (^# equal contribution) 

• Azzi, C.^#, Aeschimann, F.^#, Neagu, A., Großhans, H.^* (2020) A branched heterochronic pathway directs juvenile-to-adult transition through two LIN-29 isoforms. eLIFE. 9: e53387. https://doi.org/10.7554/elife.53387 (^# equal contribution) 

• Pereira, L., Aeschimann, F., Wang, C., Lawson, H., Serrano-Saiz, E., Portman, D.S., Großhans, H., and Hobert, O.^* (2019) Timing mechanism of sexually dimorphic nervous system differentiation. eLIFE 8: e42078. https://doi.org/10.7554/elife.42078
  Preview: Perry & Desplan (2019) eLIFE 8: e41523. https://doi.org/10.7554/eLife.41523

• Kumari, P.^#, Aeschimann, F.^#, Gaidatzis, D.^#, Keusch, J.J.^#, Ghosh, P., Neagu, A., Pachulska-Wieczorek, K., Bujnicki, J.M., Gut, H.^*, Großhans, H., and Ciosk, R.^* (2018) Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition. Nat. Commun. 9: 1549. https://doi.org/10.1038/s41467-018-03920-7

• Brancati, G., and Großhans, H.^* (2018). An interplay of miRNA abundance and target site architecture determines miRNA activity and specificity. Nucleic Acids Res. 46: 3259–3269. https://doi.org/10.1093/nar/gky201
  Highlighted in NAR Breakthrough Article
  Recommended Article: F1000Prime: https://doi.org/10.1093/nar/gky201 
  
• de la Mata, M.^*, and Großhans, H.^* (2018). Turning the table on miRNAs. Nature Struct. Mol. Biol. 25: 195–197. https://doi.org/10.1038/s41594-018-0040-x

• Miki, T.S.^#,*, Carl, S.H. ^#, and Großhans, H.^* (2017). Two distinct transcription termination modes dictated by promoters. Genes Dev. 31: 1870-1879. https://doi.org/10.1101/gad.301093.117
  Highlighted in: Otto, Nat. Rev. Genet. (2017) https://doi.org/10.1038/nrg.2017.93
  Recommended Article: F1000: https://doi.org/10.1101/gad.301093.117)

• Malone, B., Atanassov, I., Aeschimann, F., Li, X., Großhans, H., and Dieterich, C.^* (2017). Bayesian prediction of RNA translation from ribosome profiling. Nucleic Acids Res. 45: 2960-2972. https://doi.org/10.1093/nar/gkw1350

• Aeschimann, F., Kumari, P., Bartake, F., Gaidatzis, D., Xu, L., Ciosk, R., and Großhans, H.^* (2017). LIN41 post-transcriptionally silences mRNAs by two distinct and position-dependent mechanisms. Mol. Cell 65: 476–489. https://doi.org/10.1016/j.molcel.2016.12.010
  Highlighted in: Hand & Bazzini, Mol. Cell 65: 375-377;
  Editor’s Choice: Sci. Signal 10: https://doi.org/10.1126/scisignal.aam9537;
  Recommended Article: F1000: https://doi.org/10.1016/j.molcel.2016.12.010) 

• Miki, T.S., Carl, S.H., Stadler, M.B., and Großhans, H.^* (2016). XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans. PLoS Genet. 12: e1006313. https://doi.org/10.1371/journal.pgen.1006313

• Richter, H., Katic, I., Gut, H., and Großhans, H.^* (2016). Structural Basis and Function of XRN2-Binding by XTB Domains. Nat. Struct. Mol. Biol. 23: 164-71. https://doi.org/10.1038/nsmb.3155

• Aeschimann, F., Xiong, J., Arnold, A., Dieterich, C.^*, and Großhans, H.^* (2015). Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling. Methods 85: 75-89. https://doi.org/10.1016/j.ymeth.2015.06.013

• Ecsedi, M., Rausch, M., and Großhans, H.^* (2015). The let-7 microRNA directs vulval development through a single target. Dev. Cell 32: 335-44. https://doi.org/10.1016/j.devcel.2014.12.018

• Rüegger, S., Miki, T.S., Hess, D., and Großhans, H.^* (2015) The ribonucleotidyl transferase USIP-1 acts with SART3 to promote U6 snRNA recycling. Nucleic Acids Res. 43: 3344-57. https://doi.org/10.1093/nar/gkv196

• de la Mata, M., Gaidatzis, D., Vitanescu, M., Stadler, M.B., Wentzel, C., Scheiffele, P., Filipowicz, W.,^* and Großhans, H.^* (2015). Potent degradation of neuronal miRNAs induced by highly complementary targets. EMBO Rep. 16: 500-11. https://doi.org/10.15252/embr.201540078

• Rausch, M.^#, Ecsedi, M.^#, Bartake, H., and Großhans, H.^* (2015). A genome-wide screen reveals widespread function of cell cycle genes in let-7 miRNA activity. Dev. Biol. 401: 276-86. https://doi.org/10.1016/j.ydbio.2015.02.013

• Miki, T.S.^#, Rügger, S.^#, Gaidatzis, D., Stadler, M., and Großhans, H.^* (2014). Engineering of a conditional allele reveals multiple roles of XRN2 in C. elegans development and substrate specificity in microRNA turnover. Nucleic Acids Res. 42: 4056-67. https://doi.org/10.1093/nar/gkt1418

• Miki, T.S., Richter, H. ^#, Rüegger, S.^#, and Großhans, H.^* (2014). PAXT-1 promotes XRN2 activity by stabilizing it through a conserved domain. Mol. Cell 53: 351-560. https://doi.org/10.1016/j.molcel.2014.01.001

• Hendriks, G.-J.^#, Gaidatzis, D. ^#, Aeschimann, F., and Großhans, H.^* (2014). Extensive oscillatory gene expression during C. elegans development. Mol. Cell 53: 380–392. https://doi.org/10.1016/j.molcel.2013.12.013
  Highlighted in Laxman, S. et al., Mol Cell 53:363-364; Recommended Article: F1000: https://doi.org/10.1016/j.molcel.2013.12.013)

2013

• Katic, I.^* and Großhans, H.^* (2013). Targeted heritable mutation and gene conversion by Cas9-CRISPR in Caenorhabditis elegans. Genetics 195: 1173-1176. https://doi.org/10.1534/genetics.113.155754

• Bossé, G.D., Rüegger, S., Ow, M.C., Vasquez-Rifo, A., Rondeau, E.L., Ambros, V.R., Großhans, H., and Simard, M.J.^* (2013). The DeCapping Scavenger enzyme DCS-1 controls microRNA levels in Caenorhabditis elegans. Mol. Cell 50: 281-287. https://doi.org/10.1016/j.molcel.2013.02.023

• Ecsedi, M., and Großhans, H.^* (2013). LIN-41/TRIM71: Emancipation of a miRNA target. Genes Dev. 27: 581-589. https://doi.org/10.1101/gad.207266.112

• Miki, T.S.^*, and Großhans, H.^* (2013). The multifunctional RNase XRN2. Biochem. Soc. Trans. 41: 825-830. https://doi.org/10.1042/bst20130001

• Rüegger, S., and Großhans, H.^* (2012). MicroRNA Turnover: When, How, and Why. Trends Biochem. Sci. 37:436-246. https://doi.org/10.1016/j.tibs.2012.07.002

• Hurschler, B.A., Harris, D.T., and Großhans, H.^* (2011). The type II poly(A)-binding protein PABP-2 genetically interacts with the let-7 miRNA and elicits heterochronic phenotypes in Caenorhabditis elegans. Nucleic Acids Res. 39: 5647-5657. https://doi.org/10.1093/nar/gkr145

• Chatterjee, S., Fasler, M., Büssing, I., Großhans, H.^* (2011). Target-mediated protection of endogenous microRNAs in C. elegans. Dev. Cell 20: 388-396. https://doi.org/10.1016/j.devcel.2011.02.008
  Highlighted in Nat. Rev. Genet. 2011

• Filipowicz, W.^*, and Großhans, H.^* (2011). The Liver-Specific MicroRNA miR-122: Biology and Therapeutic Potential. In Gasser, S., Li, E. (eds.) Epigenetics and Disease – Pharmaceutical Opportunities. Prog. Drug Res. 67: 221-238.
  
• Großhans, H., & Chatterjee, S. (2011). MicroRNases and the Regulated Degradation of Mature Animal miRNAs. Adv Exp Med Biol. 700, 140–55. https://doi.org/10.1007/978-1-4419-7823-3_12

• Jovanovic, M., Reiter, L., Picotti, P., Lange, V., Bogan, E., Hurschler, B.A., Blenkiron, C.; Lehrbach, N.J., Ding, X.C., Weiss, M., Schrimpf, S.P., Miska, E.A., Großhans, H., Aebersold, R., Hengartner, M.O.^* (2010). A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. Nat. Methods 7: 837–842. https://doi.org/10.1038/nmeth.1504

• Büssing, I., Yang, J.S., Lai, E.C., and Großhans, H.^* (2010). The nuclear export receptor XPO-1 supports primary miRNA processing in C. elegans and Drosophila EMBO J. 29: 1830-1839. https://doi.org/10.1038/emboj.2010.82

• Großhans, H.^*, and Büssing, I. (2010). MicroRNA biogenesis takes another single hit from microsatellite instability. Cancer Cell 18: 295-297. https://doi.org/10.1016/j.ccr.2010.10.005 (Preview)

• Großhans, H. (ed.) (2010). Regulation of microRNAs. Adv. Exp. Med. Biol. Vol. 700

• Großhans, H.^*, and Chatterjee, S. (2010). MicroRNases and the regulated degradation of mature animal miRNAs. Adv. Exp. Med. Biol. 700: 140-155

• Großhans, H.^*, and Müllner, A.E. (2010). MicroRNAs in C. elegans development. Mol. Med. Medicinal Chem. 1: 54-94

• Hurschler, B.A., Ding, X.C., and Großhans, H.^* (2010). Translational Control of Endogenous MicroRNA Target Genes in C. elegans. Rhoads, R.E. (ed.): miRNA Regulation of the Translational Machinery. Prog. Mol. Subcell. Biol. 50: 21-40. https://doi.org/10.1007/978-3-642-03103-8_2

• Chatterjee, S., and Großhans, H.^* (2009). Active turnover modulates mature microRNA activity in C. elegans. Nature 461: 546-549. https://doi.org/10.1038/nature08349 (Faculty of 1,000 “Must Read”)

• Ding, X.C., and Großhans, H.^* (2009). Repression of C. elegans microRNA targets at the initiation level of translation requires GW182 proteins. EMBO J. 28: 213-222. https://doi.org/10.1038/emboj.2008.275

• Ding, X.C., Weiler, J., and Großhans, H.^* (2009). Regulating the regulators: mechanisms controlling the maturation of microRNAs. Trend Biotechnol. 27:27-36. https://doi.org/10.1016/j.tibtech.2008.09.006

• Großhans, H.^* and Svoboda, P.^* (2007). miRNAs, siRNAs, piRNAs – Kleine Wiener Ribonukleinsäuren. Bioessays 29:940-943. https://doi.org/10.1002/bies.20631

• Großhans, H.^* (2007). An in vivo perspective on microRNAs: Lessons from the worm In: MicroRNAs: Biology, Function and Expression. Clarke, N.J., and Sanseau, P.X. (eds.), pp. 127-155, DNA Press, Eagleville, PA

• Großhans, H., Johnson, T., Reinert, K.L., Gerstein, M., and Slack, F.J.^* (2005). The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev. Cell 8: 321-330. https://doi.org/10.1016/j.devcel.2004.12.019

• Johnson, S.M., Großhans, H., Shingara, J., Byrom, M., Jarvis, R., Cheng, A., Labourier, E., Reinert, K.L., Brown, D., and Slack, F.J.^* (2005). RAS is regulated by the let-7 microRNA family. Cell 120: 635-647. https://doi.org/10.1016/j.cell.2005.01.014

• Neumann, S., Petfalski, E., Brügger, B., Großhans, H., Wieland, F., Tollervey, D., and Hurt, E.^* (2003). Formation and nuclear export of tRNA, rRNA and mRNA is regulated by the ubiquitin ligase Rsp5p. EMBO Rep. 4: 1156-1162. https://doi.org/10.1038/sj.embor.7400026

• Großhans, H., and Slack, F.J.^* (2002). Micro-RNAs: small is plentiful J. Cell Biol. 156: 17-22. https://doi.org/10.1083/jcb.200111033

• Simos, G., Großhans, H., and Hurt, E.^* (2002). Nuclear export of tRNA. Results Probl. Cell Differ. 35, 115–31. https://doi.org/10.1007/978-3-540-44603-3_6

• Großhans, H., Lecointe, F., Grosjean, H., Hurt, E., and Simos, G.^* (2001). Pus1p-dependent tRNA pseudouridinylation becomes essential when tRNA biogenesis is compromised in yeast. J. Biol. Chem. 276: 46333-46339

• Galani, K., Großhans, H., Deinert, K., Hurt, E., and Simos, G.^* (2001). The intracellular location of two aminoacyl-tRNA synthetases depends on complex formation with Arc1p. EMBO J. 20: 6889-6898

• Großhans, H., Deinert, K., Hurt, E. and Simos, G.^* (2001). Biogenesis of the signal recognition particle involves import of SRP proteins into the nucleolus, assembly with the SRP-RNA, and Xpo1p-mediated export. J. Cell Biol. 153: 745-762

• Großhans, H., Hurt, E., and Simos, G.^* (2000). An aminoacylation-dependent nuclear tRNA export pathway in yeast. Genes Dev. 14: 830-884

• Großhans, H., Simos, G., and Hurt, E.^* (2000). Review: Transport of tRNA out of the nucleus – direct channeling to the ribosome? J. Struct. Biol. 129: 288-294

• Großhans, H.^* (2000). Gene therapy – when a simple concept meets a complex reality. Funct. Integr. Genomics 1: 142-145
  
  ^*: Corresponding author
  ^#: equal contribution