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The Tanenbaum group uses cutting-edge live-cell single molecule microscopy and new types of genetic engineering to uncover the molecular mechanisms of gene expression control in individual cells.
Our work focuses both on regulation of human genes in health and disease and on gene regulation of RNA viruses. Using our single-molecule approaches, we aim to uncover how the dynamics and heterogeneity in gene expression affects cell fate. In addition, we are developing new imaging technologies to visualize gene expression dynamics with ever increasing resolution to achieve a deep molecular understanding of these processes.
We are recruiting at multiple levels!!
–> More information at the bottom of this page
Previously, we have developed an imaging technique called “SunTag” (Tanenbaum et al., 2014, Cell), which allows us to link many GFPs to a protein molecule of interest (Fig. 1A). This GFP multimerization approach makes the fluorescence tags far brighter than was previously possible, and enables us to visualize complex biological processes with single molecule sensitivity in real-time in living cells. Using the SunTag, we have developed a method to visualize translation and degradation of single mRNA molecules in space and time (Fig. 1B) (Yan et al., 2016, Cell; Hoek et al., 2019, Mol Cell). We are employing these methods to visualize gene expression control in living cells with incredible precision and to uncover how regulatory mechanisms function at the single-molecule level. We are using a combination of quantitative single cell and single molecule fluorescence microscopy and computer simulations to look beyond cell population averages, and study how single cells tune gene expression over time and how differences in gene expression affect cell fate. For example, we have applied the SunTag translation imaging technique to study RNA quality control (Hoek et al., 2019, Mol Cell), heterogeneity in translation start site selection (Boersma et al., 2019, Cell) and post-transcriptional regulation of gene expression by small RNAs (Ruijtenberg et al., 2020, Nat Struct Mol Biol). We are currently exploring additional mechanisms of post-transcriptional gene regulation and are developing new technologies to examine gene expression control with even greater precision.
RNA viruses are among the most prevalent pathogens worldwide and are a major burden on society. RNA viruses have been studied extensively, but surprisingly little is known about the processes that occur during early viral infection. The first hours of infection are likely very important, as the outcome of the infection (e.g. is the virus able to replicate? Can the host cell detect the virus and prevent its spreading before viral replication can occur?) may be determined at the early stages of infection. Lack of understanding of early infection is largely due to a lack of highly sensitive assays for viral detection, as during the early stages only one or a few viral RNAs are present per host cell. We have developed a single-molecule imaging assay based on our SunTag technology, called virus infection real-time imaging (VIRIM) that allows detection of single viral RNAs, which is therefore uniquely suitable to study early viral infection (Boersma et al, 2020, Cell). Using VIRIM we can detect the moment of host entry of individual viruses and follow viral translation and replication in single cells. Surprisingly, we observe a large degree of heterogeneity in viral infection dynamics in different cells, with viruses rapidly replicating to high numbers in some cells, while showing no replication at all in other cells. A similar heterogeneity is observed in the host response to the infection, which is critical to fight off the virus. We are employing VIRIM to uncover the mechanisms underlying heterogeneity in infection and are trying to understand how viral and host gene expression is coordinated to optimize viral replication and anti-viral signaling, respectively. Together, these studies can serve as a starting point for the development of new targeted therapies against virus infections.
Control of gene expression is critical for cell fate and homeostasis, and is often de-regulated in diseases like cancer. To study the function of gene expression regulation, it is critical to be able to perturb it. However, modulating the expression of endogenous genes has been very challenging. In collaboration with the lab of Jonathan Weissman, we have developed a new system to modulate transcription rates of endogenous genes called CRISPR activation (CRISPRa), which can be applied both to study regulation of individual genes and to perform genome-wide functional screens. We are also developing innovative methods based on CRISPR gene targeting to study transcriptional and post-transcriptional gene regulation.
Boersma S, Rabouw HH, Bruurs LJM, [...] van Kuppeveld F*, Tanenbaum ME*
Hoek TA*, Khuperkar D*, Lindeboom RGH, [...] Tanenbaum ME
Boersma S*, Khuperkar D*, Verhagen BMP, [...] Tanenbaum ME
Yan X, Hoek TA, Vale RD and Tanenbaum ME.
Ruijtenberg S*, Sonneveld S*, Cui TJ, [...] Tanenbaum ME
Krijger PHL*, Hoek TA*, [...] de Laat W#, Tanenbaum ME#
Marvin Tanenbaum is senior group leader at the Hubrecht Institute, Investigator at Oncode Institute and Professor in the department of Bionanoscience at the TU Delft. His group studies the molecular mechanisms of gene expression control at the single-molecule level and aims to understand how control of gene expression affects important cellular decisions. The Tanenbaum group has developed several new techniques, including the SunTag fluorescence imaging system. Using the SunTag system they can directly visualize and quantify regulation of single mRNA molecules in living cells to study the dynamics and regulation of each individual mRNA in real time. Adaptation of the SunTag imaging system to RNA viruses has enabled live observation of viral infection and gene expression regulation as well. In addition, the SunTag was re-purposed to create an artificial transcription factor to precisely modulate gene expression of endogenous genes.
Scientific training and positions
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PhD student 2016-2021
Current: Postdoc, Xiaowei Zhuang, Harvard
PhD student 2016-2021
Current: Data Analist at Nationale-Nederlanden by Working Talent
PhD student 2015-2021
Current: Scientist, Screening & Assay Technologies, Genmab
Current: Postdoc, King’s College London & Cambridge University
Current: Assistant professor, University Utrecht
Current: Associate staff scientist, Netherlands Cancer Institute
We have recently developed exciting technology to visualize human and viral gene expression in live cells with single-molecule sensitivity. Supported by an ERC Consolidator grant, we are recruiting PhD students and postdocs to join these exciting projects to uncover mechanisms of human and viral gene expression control and to further push the boundaries of gene expression visualization. Our lab is located at the vibrant and very international Hubrecht Institute in Utrecht, The Netherlands. If you are interested in learning more about the available position(s), please send an email to Marvin Tanenbaum, including a CV (with grades for PhD student applicants), a coverletter and names and contact information of 2 references. Applicants should be especially excited to work in a very collaborative team-oriented environment. We are interested in applicants from a variety of backgrounds, including Biophysics, Cell Biology, Biochemistry, Virology and Computational biology.
We have several exciting projects involving a variety of topics and techniques available for Master students. Please email Marvin Tanenbaum if you are interested in a internship/rotation in the lab. We welcome students from both life sciences and physical sciences.
TransTrack was developed to analyze microscopy images obtained with the SunTag translation imaging system, and can be used to acquire translation intensity traces for single mRNA molecules.
Ribofitter was developed to determine the number of translating ribosomes and the exact time at which individual ribosomes initiate translation from intensity traces obtained with translational imaging.
Most plasmids can be found on addgene.
Multi-color single-molecule imaging uncovers extensive heterogeneity in mRNA decoding. Boersma S*, Khuperkar D*, Verhagen BMP, Sonneveld S, Grimm JB, Lavis LD and Tanenbaum ME.
Cell 2019 Jul 11;178(2):458-472.e19. doi:10.1016/j.cell.2019.05.001.
Translation and Replication Dynamics of Single RNA Viruses. Boersma S, Rabouw HH, Bruurs LJM, Pavlovič T, van Vliet ALW, Beumer J, Clevers H, van Kuppeveld FJM, Tanenbaum ME.
Cell 2020 Dec 23; 183, 1–16. doi: 10.1016/j.cell.2020.10.019.