A fascinating aspect of all cells is their complex intracellular organization. Cells are subdivided in different compartments to organize cellular functions by physically separating biological reactions.
This compartmentalization is fundamental to regulate gene expression both in space and time. To understand how cells dynamically control gene expression to adapt to changing environments, we use single molecule mRNA imaging technologies both for fixed and living cells. These methods allow us to follow the entire mRNA life, from transcription to degradation, from the nucleus to the cytoplasm. Using these tools, we measure, with high spatial and temporal resolution, each stage of gene expression in individual cells. We study the coordination between the different stages of gene expression, to understand how cells tune gene expression to improve their fitness. By looking at single cells, we can assess how gene expression noise and cell-to cell variability affect cellular functions.
Using cell cycle mRNA as a paradigm and S. cerevisiae as a model system, we study how cells coordinate mRNA localization, translation and decay to achieve precise gene expression regulation.
To study gene expression in single cells, we continuously develop fluorescence-based imaging tools to visualize single mRNAs in fixed and living cells.
For fixed cells, we developed a single molecule fluorescent in situ hybridization protocol combined to immuno-fluorescence for S. cerevisiae.
For living cells, we previously developed a new RNA tagging system (MS2V6) that allows us to tag individual mRNAs in S. cerevisiae and that, compared to previous reporters is particularly suited to tag unstable mRNAs. See: https://doi.org/10.1038/nmeth.4502 and https://doi.org/10.1038/s41596-018-0037-2
We study how the mRNA localization, translation and decay are coordinated within individual cell, by combining imaging, molecular biology, genetics and biochemistry.
We are particularly interested in understanding how cell cycle regulated genes such as the ASH1 mRNA tune their expression to control growth and maximize fitness.
Systems Biology Lab
Vrije Universiteit Amsterdam
Room O|2 01W55
De Boelelaan 1108
1081 HZ Amsterdam
FELLOWSHIPS AND AWARDS
Robert H. Singer, Evelina Tutucci and Maria Vera “RNA TAGGING SYSTEM FOR VISUALIZATION OF SINGLE mRNA MOLECULES” Provisional application to the US Patent and Trademark Office (no. 62/487,058).
18. Das, S, Vera, M, Gandin, V, Singer, RH*, Tutucci, E.* Intracellular mRNA transport and localized translation. Nat Rev Mol Cell Biol. 2021;22 (7):483-504. doi: 10.1038/s41580-021-00356-8. PubMed PMID:33837370 (*Co-corresponding author).
17. Tsuboi T, Viana MP, Xu F, Yu J, Chanchani R, Arceo XG, Tutucci E, Choi J, Chen YS, Singer RH, Rafelski SM, Zid BM. Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis. https://pubmed.ncbi.nlm.nih.gov/32762840/
16. Pichon X, Robert MC, Bertrand E, Singer RH and Tutucci E*. New generations of MS2 variants and MCP fusions to detect single mRNAs in living eukaryotic cells. Methods in Molecular Biology – RNA tagging (July 2020) (*Corresponding author). https://pubmed.ncbi.nlm.nih.gov/32710406/
15. Tutucci E* and Singer RH*. Simultaneous detection of mRNA and protein in S. cerevisiae by single molecule FISH and Immunofluorescence. Methods in Molecular Biology – RNA tagging (July 2020) (*Co-corresponding author). https://pubmed.ncbi.nlm.nih.gov/32710403/
14. Maekiniemi A, Singer RH, Tutucci E*. Single molecule mRNA fluorescent in situ hybridization combined with immunofluorescence in S. cerevisiae: Dataset and quantification (April 2020) (*Corresponding author). https://doi.org/10.1016/j.dib.2020.105511
13. Vera M, Tutucci E, and Singer RH. Imaging single mRNA molecules in mammalian cells using an optimized MS2-MCP system. Methods in Molecular Biology – Imaging Gene Expression (2019). doi: 10.1007/978-1-4939-9674-2_1
12. Infantino V*, Tutucci E*, Bagdiul I, Palancade B, Yeh Martin N, Zihlman A, Garcia-Molinero V, Silvano G and Stutz F. The mRNA export adaptor Yra1 contributes to DNA double-strand break repair through its C-box domain. PloS one 14 (4), e0206336 (2019) (*Equal contribution) https://doi.org/10.1371/journal.pone.0206336
11. Tutucci E, Vera M and Singer RH, Single mRNA detection in living S. cerevisiae using a re-engineered MS2 system. Nature Protocols (September 14, 2018) https://doi.org/10.1038/s41596-018-0037-2
10. Tutucci E and Singer RH Shining light on the demise of single mRNAs. Cell Systems, Invited commentary for the Series Principles of Systems Biology (No. 26) (February 28, 2018) https://doi.org/10.1016/j.cels.2018.02.002
9. Tutucci E, Livingston N, Wu B, Singer RH Imaging mRNA In Vivo, from birth to death. Annual review of biophysics 47 (2018) https://doi.org/10.1146/annurev-biophys-070317-033037 .
8. Tutucci E*, Vera M*, Biswas J, Garcia J, Parker R and Singer RH. An improved MS2 system for accurate reporting of the mRNA life cycle. Nature methods 15, 81-89 (January 2018) (*Equal contribution) https://doi.org/10.1038/nmeth.4502
7. Brickner DG, Sood V, Tutucci E, Coukos R, Viets K, Singer RH, Brickner JH. Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms Mol Biol Cell 27(19):2980-2993 (2016 October 1). https://doi.org/10.1091/mbc.E16-03-0174
6. Wu B, Miskolci V, Sato H, Tutucci E, Kenworthy CA, Donnelly SK, Yoon YJ, Cox D, Singer RH, Hodgson L. Synonymous modification results in high-fidelity gene expression of repetitive protein and nucleotide sequences. Genes & development 29(8):876-886, April 2015 https://doi.org/10.1101/gad.259358.115
5. Tutucci E, Stutz F. Keeping mRNPs in check during assembly and nuclear export. Nat Rev Mol Cell Biol. 2011 Jun;12(6):377-84 https://doi.org/10.1038/nrm3119
4. Iglesias N*, Tutucci E*, Gwizdek C, Vinciguerra P, Von Dach E, Corbett AH, Dargemont C, Stutz F. Ubiquitin-mediated mRNP dynamics and surveillance prior to budding yeast mRNA export. Genes Dev. 2010 Sep 1;24(17):1927-38; https://doi.org/10.1101/gad.583310 (*Equal contribution)
3. Terrile M, Appolloni I, Calzolari F, Perris R, Tutucci E, Malatesta P. PDGF-B-driven gliomagenesis can occur in the absence of the proteoglycan NG2. BMC Cancer. 2010 Oct 12; 10:550 https://doi.org/10.1186/1471-2407-10-550
2. Appolloni I, Calzolari F, Tutucci E, Caviglia S, Terrile M, Corte G, Malatesta P. PDGF-B induces a homogeneous class of oligodendrogliomas from embryonic neural progenitors. Int J Cancer. 2009 May 15;124(10):2251-9; https://doi.org/10.1002/ijc.24206
1. Calzolari F, Appolloni I, Tutucci E, Caviglia S, Terrile M, Corte G, Malatesta P. Tumor progression and oncogene addiction in a PDGF-B-induced model of gliomagenesis. Neoplasia. 2008 Dec; DOI: 10.1593/neo.08814
1. Infantino V*, Tutucci E*, Bagdiul I, Palancade B, Yeh Martin N, Zihlman A, Garcia-Molinero V, Silvano G and Stutz F. The mRNA export adaptor Yra1 contributes to DNA double-strand break repair through its C-box domain (*Equal contribution). BioRxiv (October 15th, 2018). https://doi.org/10.1101/441980
2. Tsuboi T, Viana MP, Xu F, Yu J, Chanchani R, Arceo XG, Tutucci E, Choi J, Chen YS, Singer RH, Rafelski SM, Zid BM. Mitochondrial volume fraction controls translation of nuclear-encoded mitochondrial proteins. BioRxiv (January 1st, 2019) https://doi.org/10.1101/529289
1. Tutucci E, Maekiniemi A and Singer RH. (2020), “Single molecule mRNA Fluorescent In Situ Hybridization combined to Immunofluorescence in S. cerevisiae: Dataset and quantification”, Mendeley Data, v4 http://dx.doi.org/10.17632/bcmn9cxyzs.4
For an updated list of publications see my Google Scholar web page: https://scholar.google.com/citations?user=AbW4QQ0AAAAJ&hl=en
Supervision of students (BSc and MSc)
|Tim Molenaar||Studying cell-cycle mRNA expression in S. cerevisiae using single mRNA imaging technologies||Bsc||2021||March-June|
|Lalitha Veleti||Studying cell-cycle mRNA expression in S. cerevisiae using single mRNA imaging technologies||Msc||2021||February-July|
|Sander van Otterdijk||Studying fungal biofilm development with single-cell fluorescence microscopy||Msc||2021||February-July|
|Amber Hondema||Studying cell-cycle mRNA expression in S. cerevisiae using single mRNA imaging technologies||Bsc (FALW Honours programme)||2020||August-September|
|Kim Verdaasdonk||Studying cell-cycle mRNA expression in S. cerevisiae using single mRNA imaging technologies||Msc and Literature Thesis||2020||February - October (with break due to Coronavirus)|
|Kelly van Rossum||Studying cell-cycle mRNA decay in S. cerevisiae using single mRNA imaging technologies||Msc and Literature Thesis||2020||February - October (with break due to Coronavirus)|
|Xin Lai||The Discovery of Ribosome Heterogeneity and its Implications on Human Disorders Linked to Mutations in the Translation Machinery||Literature Thesis||2019-2020||November-January|