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 H-Y, Han C-T, 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 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. Pages 183–194 in: PIWI-interacting RNAs; Methods in molecular biology, vol. 1093 (ed. Siomi MC), Humana Press, Totowa 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. Pages 1–14 in: Regulation of microRNAs; Advances in Experimental Medicine and Biology, vol. 700 (ed. Großhans H), Springer, New York 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 D V., 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