Ketting Lab
Research Publications Group Members Biography2024
Busetto V, Pshanichnaya L, Lichtenberger R, Hann S, Ketting RF and Falk S (2024) MUT-7 exoribonuclease activity and localization are mediated by an ancient domain. Nucleic Acids Res , 52:9076-9091 Link
Haase AD*, Ketting RF*, Lai EC*, van Rij RP*, Siomi M*, Svoboda P*, van Wolfswinkel JC* and Wu PH* (2024) PIWI-interacting RNAs: who, what, when, where, why, and how. EMBO J , 43:5335–5339 (*indicates joint contribution) Link
2023
Bronkhorst AW, Lee CY, Möckel MM, Ruegenberg S, de Jesus Domingues AM, Sadouki S, Piccinno R, Sumiyoshi T, Siomi MC, Stelzl L, Luck K and Ketting RF (2023) An extended Tudor domain within Vreteno interconnects Gtsf1L and Ago3 for piRNA biogenesis in Bombyx mori. EMBO J , 42:e114072 Link
Podvalnaya N, Bronkhorst A, Lichtenberger R, Hellmann S, Nischwitz E, Falk T, Karaulanov E, Butter F, Falk S and Ketting RF. (2023) piRNA processing by a trimeric Schlafen-domain nuclease. Nature , https://doi.org/10.1038/s41586-023-06588-2 (# indicates joint correspondence) Link
Seistrup AS, Choppin M, Govind S, Feldmeyer B, Kever M, Karaulanov E, Séguret A, Karunanithi S, Almeida M V, Ketting RF# and Foitzik S# (2023) Age- and caste-independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus. Mol Ecol , 32:6027–6043 (#indicates joint correspondence) Link
2022
Marnik EA*, Almeida MV*, Cipriani PG*, Chung G, Caspani E, Karaulanov E, Gan HH, Zinno J, Isolehto IJ, Kielisch F, Butter F, Sharp CS, Flanagan RM, Bonnet FX, Piano F, Ketting RF#, Gunsalus KC# and Updike DL# (2022) The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline. PLOS Genet , 18:e1010245 (*indicates joint contribution, #indicates joint correspondence) Link
Schreier J and Ketting RF (2022) How stress can affect your sex appeal. Dev Cell , 57:291-292 Link
Schreier J, Dietz S, Boermel M, Oorschot V, Seistrup AS, de Jesus Domingues AM, Bronkhorst AW, Nguyen DAH, Phillis S, Gleason EJ, L’Hernault SW, Phillips CM, Butter F and Ketting RF (2022) Membrane-associated cytoplasmic granules carrying the Argonaute protein WAGO-3 enable paternal epigenetic inheritance in Caenorhabditis elegans. Nat Cell Biol , 24:217–229 Link
2021
Dietz S*, Almeida MV*, Nischwitz E, Schreier J, Viceconte N, Fradera-Sola A, Renz C, Ceron-Noriega A, Ulrich HD, Kappei D, Ketting RF and Butter F (2021) The double-stranded DNA-binding proteins TEBP-1 and TEBP-2 form a telomeric complex with POT-1 Nat Commun , 12:2668 (*indicates joint contribution) Link
Gudipati RK, Braun K, Gypas F, Hess D, Schreier J, Carl SH, Ketting RF and Großhans H (2021) Protease-mediated processing of Argonaute proteins controls small RNA association. Mol Cell , 81:2388-2402.e8 Link
Ketting RF and Cochella L (2021) Concepts and functions of small RNA pathways in C. elegans. Curr Top Dev Biol , 144:45-89 Link
Perez-Borrajero C, Podvalnaya N*, Holleis K*, Lichtenberger R, Karaulanov E, Simon B, Basquin J, Hennig J# , Ketting RF# and Falk S# (2021) Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans. Genes Dev , 35:1304-1323 (*indicates joint contribution, #indicates joint correspondence) Link
Placentino M, de Jesus Domingues AM, Schreier J, Dietz S, Hellmann S, de Albuquerque BFM, Butter F and Ketting RF (2021) Intrinsically disordered protein PID-2 modulates Z granules and is required for heritable piRNA-induced silencing in the Caenorhabditis elegans embryo EMBO J , 40:e105280 Link
Redl S*, de Jesus Domingues AM*, Caspani E, Möckel S, Salvenmoser W, Mendez-Lago M and Ketting RF (2021) Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish. Development , 148:dev193060 (*indicates joint contribution) Link
Volz AK, Frei A, Kretschmer V, de Jesus Domingues AM, Ketting RF, Ueffing M, Boldt K, Krämer-Albers EM and May-Simera HL (2021) Bardet-Biedl syndrome proteins modulate the release of bioactive extracellular vesicles. Nat Commun , 12:5671 Link
2020
Ketting RF and Cochella L (2020) Concepts and functions of small RNA pathways in C. elegans. in: Current Topics in Developmental Biology, Academic Press, 144:45–89 Link
Manage KI, Rogers AK, Wallis DC, Uebel CJ, Anderson DC, Nguyen DAH, Arca K, Brown KC, Cordeiro Rodrigues RJ, de Albuquerque BFM, Ketting RF, Montgomery TA and Phillips CM (2020) A Tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans.Elife, 9:e56731 Link
2019
Almeida MV, Andrade-Navarro MA and Ketting RF (2019) Function and evolution of nematode RNAi pathways. Non-Coding RNA, 5:8 Link
Almeida MV, de Jesus Domingues AM and Ketting RF (2019) Maternal and zygotic gene regulatory effects of endogenous RNAi pathways. PLOS Genet, 15:e1007784 Link
Almeida MV, de Jesus Domingues AM, Lukas H, Mendez-Lago M and Ketting RF (2019) RppH can faithfully replace TAP to allow cloning of 5′-triphosphate carrying small RNAs. MethodsX, 6:265–272 Link
Cordeiro Rodrigues RJ, de Jesus Domingues AM, Hellmann S, Dietz S, de Albuquerque BFM, Renz C, Ulrich HD, Sarkies P, Butter F and Ketting RF (2019) PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability. Genes Dev, 33:857–870 Link
2018
Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F and Ketting RF (2018) GTSF‐1 is required for formation of a functional RNA‐dependent RNA Polymerase complex in Caenorhabditis elegans. EMBO J, 37:e99325 Link
Bronkhorst AW and Ketting RF (2018) Trimming it short: PNLDC1 is required for piRNA maturation during mouse spermatogenesis. EMBO Rep, 19:e45824 Link
Kaaij LJT, van der Weide RH, Ketting RF and de Wit E (2018) Systemic loss and gain of chromatin architecture throughout zebrafish development. Cell Rep, 24:1–10.e4 Link
Roovers EF*, Kaaij LJT*, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A and Ketting RF (2018) Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specification. Dev Cell, 46:285–301.e9 (*indicates joint contribution) Link
2017
Lebedeva S, de Jesus Domingues AM, Butter F and Ketting RF (2017) Characterization of genetic loss-of-function of Fus in zebrafish. RNA Biol, 14:29–35 Link
2016
Kaaij LJT, Mokry M, Zhou M, Musheev M, Geeven G, Melquiond ASJ, de Jesus Domingues AM, de Laat W, Niehrs C, Smith AD and Ketting RF (2016) Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol, 17:146 Link
San B, Chrispijn ND, Wittkopp N, van Heeringen SJ, Lagendijk AK, Aben M, Bakkers J, Ketting RF and Kamminga LM (2016) Normal formation of a vertebrate body plan and loss of tissue maintenance in the absence of ezh2. Sci Rep, 6:24658 Link
2015
de Albuquerque BFM, Placentino M and Ketting RF (2015) Maternal piRNAs are essential for germline development following de novo establishment of endo-siRNAs in Caenorhabditis elegans. Dev Cell, 34:448–456 Link
Gebert D, Ketting RF, Zischler H and Rosenkranz D (2015) piRNAs from pig testis provide evidence for a conserved role of the piwi pathway in post-transcriptional gene regulation in mammals. PLOS One, 10:e0124860 Link
Prakash K, Fournier D, Redl S, Best G, Borsos M, Tiwari VK, Tachibana-Konwalski K, Ketting RF, Parekh SH, Cremer C and Birk UJ (2015) Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes. Proc Natl Acad Sci USA, 112:14635–14640 Link
Roovers EF, Rosenkranz D, Mahdipour M, Han CT, He N, Chuva de Sousa Lopes SM, van der Westerlaken LAJ, Zischler H, Butter F, Roelen BAJ and Ketting RF (2015) Piwi proteins and piRNAs in mammalian oocytes and early embryos. Cell Rep, 10:2069–2082 Link
Rosenkranz D, Han C-T, Roovers EF, Zischler H and Ketting RF (2015) Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genomics Data, 5:309–313 Link
Rosenkranz D, Rudloff S, Bastuck K, Ketting RF and Zischler H (2015) Tupaia small RNAs provide insights into function and evolution of RNAi-based transposon defense in mammals. RNA, 21:911–922 Link
2014
de Albuquerque BFM, Luteijn MJ, Cordeiro Rodrigues RJ, van Bergeijk P, Waaijers S, Kaaij LJT, Klein H, Boxem M and Ketting RF (2014) PID-1 is a novel factor that operates during 21U-RNA biogenesis in Caenorhabditis elegans. Genes Dev, 28:683–688 Link
Huang H-Y and Ketting RF (2014) Isolation of Zebrafish gonads for RNA isolation. Methods Mol Biol, 1093:183-94 Link
Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D and Helm M (2014) Profiling of RNA modifications by multiplexed stable isotope labelling. Chem Commun, 50:3516–3518 Link
Phillips CM, Montgomery BE, Breen PC, Roovers EF, Rim Y-S, Ohsumi TK, Newman MA, van Wolfswinkel JC, Ketting RF, Ruvkun G and Montgomery TA (2014) MUT-14 and SMUT-1 DEAD box RNA helicases have overlapping roles in germline RNAi and endogenous siRNA formation. Curr Biol, 24:839–844 Link
Swarts DC, Makarova K, Wang Y, Nakanishi K, Ketting RF, Koonin E V, Patel DJ and van der Oost J (2014) The evolutionary journey of Argonaute proteins. Nat Struct Mol Biol, 21:743–753 Link
2013
Basten SG, Davis EE, Gillis AJM, van Rooijen E, Stoop H, Babala N, Logister I, Heath ZG, Jonges TN, Katsanis N, Voest EE, van Eeden FJ, Medema RH, Ketting RF, Schulte-Merker S, Looijenga LHJ and Giles RH (2013) Mutations in LRRC50 predispose zebrafish and humans to seminomas. PLOS Genet, 9:e1003384 Link
de Albuquerque BFM and Ketting RF (2013) Is this mine? Small RNAs help to decide. Dev Cell, 27:599–601 Link
Kaaij LJT, Hoogstrate SW, Berezikov E and Ketting RF (2013) piRNA dynamics in divergent zebrafish strains reveal long-lasting maternal influence on zygotic piRNA profiles. RNA, 19:345–356 Link
Kaaij LTJ, van de Wetering M, Fang F, Decato B, Molaro A, van de Werken HJG, van Es JH, Schuijers J, de Wit E, de Laat W, Hannon GJ, Clevers HC, Smith AD and Ketting RF (2013) DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus. Genome Biol, 14:R50 Link
Luteijn MJ and Ketting RF (2013) PIWI-interacting RNAs: From generation to transgenerational epigenetics. Nat Rev Genet, 14:523–534 Link
2012
Kamminga LM, van Wolfswinkel JC, Luteijn MJ, Kaaij LJT, Bagijn MP, Sapetschnig A, Miska EA, Berezikov E and Ketting RF (2012) Differential impact of the HEN1 homolog HENN-1 on 21U and 26G RNAs in the germline of Caenorhabditis elegans. PLOS Genet, 8:e1002702 Link
Luteijn MJ, van Bergeijk P, Kaaij LJT, Almeida MV, Roovers EF, Berezikov E and Ketting RF (2012) Extremely stable Piwi-induced gene silencing in Caenorhabditis elegans. EMBO J, 31:3422–3430 Link
2011
Huang H-Y, Houwing S, Kaaij LJT, Meppelink A, Redl S, Gauci S, Vos H, Draper BW, Moens CB, Burgering BM, Ladurner P, Krijgsveld J, Berezikov E and Ketting RF (2011) Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. EMBO J, 30:3298–3308 Link
Kamminga LM and Ketting RF (2011) RNAi genes pave their own way. Genes Dev, 25:529–533 Link
Ketting RF (2011) The many faces of RNAi. Dev Cell, 20:148–161 Link
2010
Corrêa RL, Steiner FA, Berezikov E and Ketting RF (2010) MicroRNA–directed siRNA biogenesis in Caenorhabditis elegans. PLOS Genet, 6:e1000903 Link
Kaaij LJT and Ketting RF (2010) Dcr1 tracked down. Dev Cell, 18:6–7 Link
Kamminga LM, Luteijn MJ, den Broeder MJ, Redl S, Kaaij LJT, Roovers EF, Ladurner P, Berezikov E and Ketting RF (2010) Hen1 is required for oocyte development and piRNA stability in zebrafish. EMBO J, 29:3688–3700 Link
Ketting RF (2010) microRNA biogenesis and function. Advances in Experimental Medicine and Biology, 700:1-14 Link
van Wolfswinkel JC and Ketting RF (2010) The role of small non-coding RNAs in genome stability and chromatin organization. J Cell Sci, 123:1825–1839 Link
2009
Claycomb JM, Batista PJ, Pang KM, Gu W, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF, Conte D and Mello CC (2009) The argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell, 139:123–134 Link
den Broeder MJ, van der Linde H, Brouwer JR, Oostra BA, Willemsen R and Ketting RF (2009) Generation and characterization of Fmr1 knockout zebrafish. PLOS One, 4:e7910 Link
Ketting RF (2009) Semiconserved regulation of mesendoderm differentiation by microRNAs. Dev Cell, 16:487–488 Link
Steiner FA, Okihara KL, Hoogstrate SW, Sijen T and Ketting RF (2009) RDE-1 slicer activity is required only for passenger-strand cleavage during RNAi in Caenorhabditis elegans. Nat Struct Mol Biol, 16:207–211 Link
van Wolfswinkel JC, Claycomb JM, Batista PJ, Mello CC, Berezikov E and Ketting RF (2009) CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs. Cell, 139:135–148 Link
2008
Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, Sapetschnig A, Buhecha HR, Gilchrist MJ, Howe KL, Stark R, Matthews N, Berezikov E, Ketting RF, Tavaré S and Miska EA (2008) Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell, 31:79–90 Link
Houwing S, Berezikov E and Ketting RF (2008) Zili is required for germ cell differentiation and meiosis in zebrafish. EMBO J, 27:2702–2711 Link
2007
Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov DV, Blaser H, Raz E, Moens CB, Plasterk RHA, Hannon GJ, Draper BW and Ketting RF (2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell, 129:69–82 Link
Ketting RF (2007) A dead end for microRNAs. Cell, 131:1226–1227 Link
Kloosterman WP, Lagendijk AK, Ketting RF, Moulton JD and Plasterk RHA (2007) Targeted inhibition of miRNA maturation with morpholinos reveals a role for miR-375 in pancreatic islet development. PLOS Biol, 5:e203 Link
Steiner FA, Hoogstrate SW, Okihara KL, Thijssen KL, Ketting RF, Plasterk RHA and Sijen T (2007) Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nat Struct Mol Biol, 14:927–933 Link