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

Faculty of Science

Swammerdam Institute for Life Sciences

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
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
- refereed (15)
2024

Noviello, G., & Gjaltema, R. A. F. (2024). Fine-Tuning the Epigenetic Landscape: Chemical Modulation of Epigenome Editors. In A. Jeltsch, & M. G. Rots (Eds.), Epigenome Editing: Methods and Protols (2nd ed., pp. 57-77). (Methods in Molecular Biology; Vol. 2842). Humana Press. https://doi.org/10.1007/978-1-0716-4051-7_3 [details]
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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

Noviello, G., Gjaltema, R. A. F., & Schulz, E. G. (2023). CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression. Nature Communications, 14, Article 3225. https://doi.org/10.1038/s41467-023-38909-4 [details]
Downloads
CasTuner is a degron and CRISPR Cas-based toolkit
Supplementary files
Supplementary Information
Reporting Summary
Peer Review File
Description of Additional Supplementary Files
Supplementary Data 1
Supplementary Data 2
Supplementary Data 3
Supplementary Data 4
Souce Data

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

Gjaltema, R. A. F., & Rots, M. G. (2020). Advances of epigenetic editing. Current opinion in chemical biology, 57, 75-81. https://doi.org/10.1016/j.cbpa.2020.04.020

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

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