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Swammerdam Institute for Life Sciences Swammerdam Institute for Life Sciences

Dr. R.A.F. (Rutger) Gjaltema

Faculty of Science
SILS/Molecular Plant Pathology
Photographer: David Ausserhofer
Visiting address
  • Science Park 904
  • Room number: C2.103
Postal address
  • Postbus 1212
    1000 BE Amsterdam
Contact details
  • Research area

    The Gjaltema Lab

    Our lab specializes in epigenetic cell memory, a biochemical layer of information that preserves gene expression networks and defines a cell’s identity. We focus on how this memory is faithfully maintained across cell generations and how we can introduce new, lasting epigenetic memories or restore those that have been lost.

    Our research primarily targets:

    • Identification of New Regulators: We investigate novel regulators and regulatory pathways that influence the inheritance of epigenetic memory across cell generations following mitosis, with a particular focus on their role in early embryonic development and the pathogenesis of inflammation-related diseases. A significant part of our research is dedicated to understanding how Polycomb-derived repressive histone marks are inherited in this context, as well as the role of the nucleolus and linker histone H1 subtypes in this process
    • Advancing Epigenetic editing technology: We develop cutting-edge epigenetic editing technologies based on the CRISPR-dCas platform to introduce or remove epigenetic marks. These tools are designed to establish new, lasting epigenetic memories at target loci or erase existing ones.

    These comprehensive approaches aim to deepen our understanding of epigenetic memory mechanisms and their manipulation for future therapeutic purposes.

    Our Toolbox

    We are a technology-driven lab that applies and develops cutting-edge methods to measure transcription and epigenetic parameters, simulate epigenetic memory, deplete proteins in a (spatio)temporal manner, and perform CRISPR screens to identify novel regulators of gene regulatory processes. We use these tools in various cellular model systems, including mouse embryonic stem cells under different differentiation conditions, human cancer cells, and human primary cells, to address fundamental biological questions.

  • Student projects

    We frequently have opportunities for BSc and MSc students to join our lab and get trained in various disciplines in ongoing projects. As availability is limited, please reach out to us well in advance for more details via r.a.f.gjaltema@uva.nl

  • Team members

    Current members

    Reza Shoghi MSc (PhD Candidate)

    Quint van Loosen MSc (PhD candidate; copromoter with Prof. Dr. Verschure)

    Anna van den Berg van Saparoea MSc (Research technician; co-supervisor with Prof. Dr. Verschure)

     

    Alumni

    Tjomme Nauta (MSc, University of Amsterdam | December 2023 - August 2024

    Judith Portillo Bescos (Bsc, University of Barcelona, Erasmus) | February 2024 - July 2024

    Sofia Moreno Hoffmann (MSc, University of Amsterdam) | January - October 2023

    Jip van der Heijden (BSc, Radboud University Nijmegen) | Februari - June  2023

      

  • Biography

    Rutger Gjaltema earned his Ph.D. with honors from the University of Groningen, the Netherlands  (2011-2016) with the thesis titled 'Modifications of collagen and chromatin in ECM-related disease: Uncovering therapeutic targets for fibrosis and cancer.' During this period, he concentrated on the epigenetic regulation of genes in fibrosis and cancer. Specifically, he developed epigenome editing tools to regulate PLOD2 expression in cancer cells and fibrotic fibroblasts. Additionally, he unraveled several molecular mechanisms governing fibrosis and Bruck syndrome. This research was conducted in the labs of Prof. Dr. Marianne Rots and Prof. Dr. Ruud Bank at the University Medical Center Groningen.

    For his postdoctoral period (2016-2022), Rutger joined the lab of Dr. Edda Schulz at the Max Planck Institute for Molecular Genetics in Berlin, Germany. There, he investigated the cis-regulatory landscape of X-chromosome inactivation during early embryonic development. His research identified insights into the regulation of Xist, a crucial player in X-chromosome inactivation in females. Importantly, he discovered a new long non-coding RNA locus (Xert) with a superenhancer, acting as the primary cis-regulatory cue for Xist and influencing random X-chromosome inactivation in mouse embryonic stem cells.

    In 2022, Rutger took on the position of Assistant Professor of Epigenetics in the Molecular & Cellular Epigenetics group at the Swammerdam Institute for Life Sciences, University of Amsterdam. In this role, he dedicates his time to both research and teaching across various programs within the Faculty of Science (UvA).

  • Publications
    Publications
  • Publications

    2024

    • van den Berg van Saparoea, A. C. H., van Loosen, Q. C., Sarno, F., Ntini, E., Rots, M. G., Gjaltema, R. A. F., & Verschure, P. J. (2024). Plasmid Delivery and Single-Cell Plasmid Expression Analysis for CRISPR/dCas9-Based Epigenetic Editing. In A. Jeltsch, & M. G. Rots (Eds.), Epigenome Editing: Methods and Protocols (2nd ed., pp. 255-265). (Methods in molecular biology; Vol. 2842). Humana Press. https://doi.org/10.1007/978-1-0716-4051-7_13 [details]

    2023

    2022

    • Gjaltema, R. A. F., Schwämmle, T., Kautz, P., Robson, M., Schöpflin, R., Ravid Lustig, L., Brandenburg, L., Dunkel, I., Vechiatto, C., Ntini, E., Mutzel, V., Schmiedel, V., Marsico, A., Mundlos, S., & Schulz, E. G. (2022). Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus. Molecular Cell, 82(1), 190-208.e17. https://doi.org/10.1016/j.molcel.2021.11.023

    2021

    • Vanchin, B., Sol, M., Gjaltema, R. A. F., Brinker, M., Kiers, B., Pereira, A. C., Harmsen, M. C., Moonen, J.-R. A. J., & Krenning, G. (2021). Reciprocal regulation of endothelial-mesenchymal transition by MAPK7 and EZH2 in intimal hyperplasia and coronary artery disease. Scientific Reports, 11(1), 17764. https://doi.org/10.1038/s41598-021-97127-4

    2020

    2018

    • Gjaltema, R. A. F., & Schulz, E. G. (2018). CRISPR/dCas9 Switch Systems for Temporal Transcriptional Control. Methods in molecular biology (Clifton, N.J.), 1767, 167-185. https://doi.org/10.1007/978-1-4939-7774-1_8

    2017

    • Gjaltema, R. A. F., & Bank, R. A. (2017). Molecular insights into prolyl and lysyl hydroxylation of fibrillar collagens in health and disease. Critical Reviews in Biochemistry and Molecular Biology, 52(1), 74-95. https://doi.org/10.1080/10409238.2016.1269716
    • Leus, N. G. J., van den Bosch, T., van der Wouden, P. E., Krist, K., Ourailidou, M. E., Eleftheriadis, N., Kistemaker, L. E. M., Bos, S., Gjaltema, R. A. F., Mekonnen, S. A., Bischoff, R., Gosens, R., Haisma, H. J., & Dekker, F. J. (2017). HDAC1-3 inhibitor MS-275 enhances IL10 expression in RAW264.7 macrophages and reduces cigarette smoke-induced airway inflammation in mice. Scientific Reports, 7, 45047. https://doi.org/10.1038/srep45047
    • Piersma, B., Wouters, O. Y., de Rond, S., Boersema, M., Gjaltema, R. A. F., & Bank, R. A. (2017). Ascorbic acid promotes a TGFβ1-induced myofibroblast phenotype switch. Physiological Reports, 5(17). https://doi.org/10.14814/phy2.13324
    • Song, J., Cano-Rodriquez, D., Winkle, M., Gjaltema, R. A. F., Goubert, D., Jurkowski, T. P., Heijink, I. H., Rots, M. G., & Hylkema, M. N. (2017). Targeted epigenetic editing of SPDEF reduces mucus production in lung epithelial cells. American journal of physiology. Lung cellular and molecular physiology, 312(3), L334-L347. https://doi.org/10.1152/ajplung.00059.2016

    2016

    • Cano-Rodriguez, D., Gjaltema, R. A. F., Jilderda, L. J., Jellema, P., Dokter-Fokkens, J., Ruiters, M. H. J., & Rots, M. G. (2016). Writing of H3K4Me3 overcomes epigenetic silencing in a sustained but context-dependent manner. Nature Communications, 7, 12284. https://doi.org/10.1038/ncomms12284
    • Gjaltema, R. A. F., van der Stoel, M. M., Boersema, M., & Bank, R. A. (2016). Disentangling mechanisms involved in collagen pyridinoline cross-linking: The immunophilin FKBP65 is critical for dimerization of lysyl hydroxylase 2. Proceedings of the National Academy of Sciences of the United States of America, 113(26), 7142-7. https://doi.org/10.1073/pnas.1600074113

    2015

    • Gjaltema, R. A. F., de Rond, S., Rots, M. G., & Bank, R. A. (2015). Procollagen Lysyl Hydroxylase 2 Expression Is Regulated by an Alternative Downstream Transforming Growth Factor β-1 Activation Mechanism. The Journal of Biological Chemistry, 290(47), 28465-28476. https://doi.org/10.1074/jbc.M114.634311
    • Maleszewska, M., Gjaltema, R. A. F., Krenning, G., & Harmsen, M. C. (2015). Enhancer of zeste homolog-2 (EZH2) methyltransferase regulates transgelin/smooth muscle-22α expression in endothelial cells in response to interleukin-1β and transforming growth factor-β2. Cellular Signalling, 27(8), 1589-1596. https://doi.org/10.1016/j.cellsig.2015.04.008
    This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list.
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