Research Groups

Stem Cell Regulation

Research in the Lansdorp lab is aimed at understanding the role of stem cells in relation to ageing. The focus is on the role of telomeres and telomerase in stem cell renewal, the role of specific helicases and specific DNA sequences in stem cell function and, more generally, on the molecular mechanisms that regulate stem cell self-renewal and differentiation. Key questions are related to the role of (epi-)genetic instability in ageing, chromatin differences between mortal and immortal stem cells and the role guanine quadruplex structures in nuclear organization and chromosome instability. 

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  • Eugene Berezikov Visit

    Group Leader of the Laboratory of Stem Cell Regulation and Mechanisms of Regeneration

    Research fields

    Stem cells, regeneration, ageing, flatworms, small RNAs

    PhD Students
    Daniil Simanov
    Jakub Wudarski
    Postdoctoral Fellows
    Stijn Mouton
    Ekaterina Ovchin
    Philipp Weissert
    Frank Beltman
    Lisa Glazenburg
  • We have developed novel techniques including single cell DNA (strand) sequencing techniques that allow accurate identification of numerical chromosomal abnormalities and specific sister chromatids in individual cells. For studies of telomere attrition and numerical chromosomal abnormalities in aging specific cells are analysed by flow cytometry and sorted as single cells. Such cells include cells from participants in the LifeLines project in Groningen (160,000 individuals). Studies of human cells are complemented using cells from patients and studies in suitable mouse models. We are specifically interested to measure telomere dysfunction and aneuploidy in stem cells and more differentiated cell types, to identify genetic and other factors regulating human leukocyte telomere length and to study the role of genetic instability and chromosomal abnormalities in cells in relation to normal human ageing and specific diseases.

    • Jan Philipp Junker, Emily S. Noe, Victor Guryev, Kevin A. Peterson, Gopi Shah, Jan Huisken, Andrew P. McMahon, Eugene Berezikov, Jeroen Bakkers, and Alexander van Oudenaarden. (2014) Genome-wide RNA Tomography. Cell.
    • Oncotarget-Negar Babae, Meriem Bourajjaj, Yijia Liu, Judy R. Van Beijnum, Francesco Cerisoli, Puthupparampil V. Scaria, Mark Verheul, Maaike P. Van Berkel, Ebel H. E. Pieters, Rick J. Van Haastert, A. Yousefi, E. Mastrobattista, Gert Storm, E. Berezikov, et all.. (2014) Systemic miRNA-7 delivery inhibits tumor angiogenesis and growth in murine xenograft glioblastoma. Oncotarget.
    • Moroz LL, Kocot KM, Citarella MR, Dosung S, Norekian TP, Povolotskaya IS, Grigorenko AP, Dailey C, Berezikov E, et all. (2014) The ctenophore genome and the evolutionary origins of neural systems.. Nature.
    • Lengerer B, Pjeta R, Wunderer J, Rodrigues M, Arbore R, Schärer L, Berezikov E, Hess MW, Pfaller K, Egger B, Obwegeser S, Salvenmoser W, Ladurner P. (2014) Biological adhesion of the flatworm Macrostomum lignano relies on a duo-gland system and is mediated by a cell type-specific intermediate filament protein.. Front Zool.
    • Moreno-Mateos MA, Barragán V, Torres B, Rodríguez-Mateo C, Méndez-Vidal C,Berezikov E, Mudduluru G, Allgayer H, Pintor-Toro JA. (2013) Novel small RNA expression libraries uncover hsa-miR-30b and hsa-miR-30c as important factors in anoikis resistance. RNA.
    • Isik M, Berezikov E. (2013) Biolistic transformation of Caenorhabditis elegans. Methods Mol Biol.
    • Janicke T, Marie-Orleach L, De Mulder K, Berezikov E, Ladurner P, Vizoso DB, Schärer L.. (2013) Sex allocation adjustment to mating group size in a simultaneous hermaphrodite. Evolution.
    • Demircan T, Berezikov E. (2013) The Hippo pathway regulates stem cells during homeostasis and regeneration of the flatworm Macrostomum lignano. Stem Cells Dev.
    • Leptidis S, El Azzouzi H, Lok SI, de Weger R, Olieslagers S, Kisters N, Silva GJ, Heymans S, Cuppen E, Berezikov E, De Windt LJ, da Costa Martins P. (2013) A deep sequencing approach to uncover the miRNOME in the human heart. PloS One.
    • Chiodin M, Børve A, Berezikov E, Ladurner P, Martinez P, Hejnol A. (2013) Mesodermal gene expression in the acoel Isodiametra pulchra indicates a low number of mesodermal cell types and the endomesodermal origin of the gonads. PloS One.
    • Kaaij LJ, Hoogstrate SW, Berezikov E, Ketting RF. (2013) piRNA dynamics in divergent zebrafish strains reveal long-lasting maternal influence on zygotic piRNA profiles. RNA.
    • Simanov D, Mellaart-Straver I, Sormacheva I, Berezikov E. (2012) The Flatworm Macrostomum lignano Is a Powerful Model Organism for Ion Channel and Stem Cell Research. Stem cells international.
    • Isik M, Berezikov E . (2012) Expression pattern analysis of microRNAs in Caenorhabditis elegans. Methods Mol Biol.
    • Berezikov E. (2011) Evolution of microRNA diversity and regulation in animals. Nat. Rev. Genet.
    • Ryazansky SS, Gvozdev VA, Berezikov E. (2011) Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila. BMC Genomics.
    • modENCODE Consortium. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science.
    • Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC. (2010) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research.
    • Isik m, Korswagen H, Berezikov E. (2010) Expression patterns of intronic microRNAs in Caenorhabditis elegans. Silenc.
    • Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC. (2010) Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nat. Genet.
    • van Wolfswinkel JC, Claycomb JM, Batista PJ, Mello CC, Berezikov E, Ketting RF. (2009) CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs. Cell.
    • de Wit E, Linsen SE, Cuppen E, Berezikov E. (2009) Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res.
    • Vreugdenhil E, Berezikov E. (2009) Fine-tuning the brain: MicroRNAs. Frontiers in Neuroendocrinology.
    • van Rij RP, Berezikov E. (2009) Small RNAs and the control of transposons and viruses in Drosophila. Trends in microbiology.
    • Schwamborn JC, Berezikov E, Knoblich JA. (2009) The TRIM-NHL protein TRIM32 activates microRNAs and prevents self-renewal in mouse neural progenitors. Cell.
    • Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC. (2007) Mammalian mirtron genes. Molecular cell.
    • Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov DV, Blaser H, Raz E, Moens CB, Plasterk RH, Hannon GJ, Draper BW, Ketting RF. (2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell.
    • Berezikov E, Thuemmler F, van Laake LW, Kondova I, Bontrop R, Cuppen E, Plasterk RH. (2006) Diversity of microRNAs in human and chimpanzee brain. Nature Genetics.
    • Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J, Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano H, Plasterk R, Cuppen E. (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Research.
    • Berezikov E, Cuppen E, Plasterk RH. (2006) Approaches to microRNA discovery. Nature Genetics.
    • Berezikov E, Plasterk RH. (2005) Camels and zebrafish, viruses and cancer: a microRNA update. Human Molecular Genetics.
    • Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH.. (2005) MicroRNA expression in zebrafish embryonic development. Science.v
    • Berezikov E, Guryev V, Cuppen E. (2005) CONREAL web server: identification and visualization of conserved transcription factor binding sites. Nucleic Acids Research.
    • Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell.
    • Berezikov E, Guryev V, Plasterk RH, Cuppen E. (2003) CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Research.
    • Berezikov E, Plasterk RH, Cuppen E. (2002) GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. Bioinformatics.
    • Berezikov E, Bucheton A, Busseau I. (2000) A search for reverse transcriptase-coding sequences reveals new non-LTR retrotransposons in the genome of Drosophila melanogaster. Genome Biology.
    • Berezikov E, Blinov AG, Scherbik S, Cox CK, Case ST. (1998) Structure and polymorphism of the Chironomus thummi gene encoding special lobe-specific silk protein, ssp160. Gene.
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