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Zhao, L., Fonseca, A., Meschichi, A., Sicard A, Rosa S. Whole-mount smFISH allows combining RNA and protein quantification at cellular and subcellular resolution. Nature Plants (2023).

Antoniou-Kourounioti RL, Anis Meschichi, Svenja Reeck, Scott Berry, Govind Menon, Yusheng Zhao, John A. Fozard, Terri L. Holmes, Huamei Wang, Matthew Hartley, Caroline Dean*, Stefanie Rosa*, Martin Howard* (2023) Integrating analog and digital modes of gene expression at Arabidopsis FLC. eLife  12:e79743. doi: 10.7554/eLife.79743.  *co-corresponding author

Meschichi A, Rosa S (2023) Plant chromatin on the move: an overview of chromatin mobility during transcription and DNA repairThe Plant Journal.

Fonseca A, Rosa S. (2023). Detection and automated quantification of nucleocytoplasmic RNA fractions in Arabidopsis using smFISH. Methods in Molecular Biology. In press

Meschichi A, Reeck S, Sicard A, Pontvianne F, Rosa S (2022) The plant-specific DDR factor SOG1 increases chromatin mobility in response to DNA damage. EMBO Reports 23:e54736

Fonseca A, Moyano T, Rosa S, Gutiérrez R (2022) Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots bioRxiv 2022.01.07.475360; doi: 10.1101/2022.01.07.475360.

Meschichi A, Ingouff M, Picart C, Mirouze M, Desset S, Gallardo F, Bystricky K, Picault N, Rosa S, Pontvianne F (2021) ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization in Planta. Frontiers in Plant Sciences 12:677849.

Meschichi A, Rosa S (2021) Visualizing and Measuring Single Locus Dynamics in Arabidopsis thaliana. Methods in Molecular Biology 2200:213-224.

Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S*, Farrona S*. (2020) Tidying-up the plant nuclear space: domains, functions, and dynamics. J Exp Bot. 71:5160-5178 doi: 10.1093/jxb/eraa282. *co-corresponding author

Qüesta JI, Antoniou-Kourounioti RL, Rosa S, Li P, Duncan S, Whittaker C, Howard M, Dean C. (2020) Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC. Genes & Development  34: 446–461.

Fritz MA, Rosa S, Sicard A. (2018) Mechanisms Underlying the Environmentally Induced Plasticity of Leaf Morphology. Front. Genetics. doi: 10.3389/fgene.2018.00478.


Rosa S. (2018) Measuring dynamics of histone proteins by photobleaching. Methods in Molecular Biology 1675:455-465. doi: 10.1007/978-1-4939-7318-7_26. 

Berry S, Rosa S, Howard M, Bühler M, Dean C. (2017) Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression. Genes and Development 31, 2115-2120. 

Duncan S, Rosa S. (2017) Gaining insight into plant gene transcription using smFISH. Transcription 9:1-5 doi: 10.1080/21541264.2017.1372043 

Ietswaart R*, Rosa S*, Wu Z*, Olsson T, Hartley M, Dean C and Howard M. (2017) Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation. Cell Systems 4, 622-635. *equally contributed 

Duncan S, Olsson T, Hartley M, Dean C and Rosa S*. (2017) Single Molecule RNA FISH in Plant Root Cells. Bio-protocols 7(8):e2240. Doi:  10.21769/BioProtoc.2240.*corresponding author

Rosa S, Duncan S, Dean C. (2016) Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression. Nature Communications 7, 13031 doi: 10.1038/ncomms13031. 

Duncan S, Olsson T, Hartley M, Dean C and Rosa S*. (2016) A method for detecting single mRNA molecules in Arabidopsis thaliana. Plant Methods 12:13, doi:10.1186/s13007-016-0114-x *corresponding author 

Rosa S*, Shaw P. (2015) Two-Photon Photoactivation to measure histone exchange dynamics in plant cells. Bio-protocol 5(20): e1628. *corresponding author 

Rosa S, Ntoukakis V, Ohmido N, Pendle A, Abranches R and Shaw P. (2014) Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single cell level. The Plant Cell 26, 4821-4833. 

Zhu D, Rosa S, Dean C. (2014) Nuclear Organization Changes and the Epigenetic Silencing of FLC during Vernalization. Journal of Molecular Biology 427, 659-69. 

Podufall J, Tian R, Knoche E, Puchkov D, Walter AM, Rosa S, Quentin C, Vukoja A, Jung N, Lampe A, Wichmann C, Böhme M, Depner H, Zhang YQ, Schmoranzer J, Sigrist SJ, Haucke V. (2014) A presynaptic role for the cytomatrix protein GIT in synaptic vesicle recycling. Cell Reports 7, 1417-25. 


Rosa S, De Lucia F, Mylne JS, Zhu D, Ohmido N, Pendle A, Kato N, Shaw P, Dean C. (2013) Physical clustering of FLC alleles during Polycomb-mediated epigenetic silencing in vernalization. Genes & Development 27, 1845-50. 

Rosa S, Shaw P. (2013) Insights into chromatin structure and dynamics in plants. Biology 2, 1378-410. 

Pires A., Rosa S., Castanheira S., Fevereiro P. and Abranches R. (2012) Expression of a recombinant human erythropoietin in suspension cell cultures of Arabidopsis, tobacco and Medicago. Plant Cell, Tissue and Organ Culture 110, 171-181.

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