Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH.

Autor:	Savulescu AF; Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7295 Cape Town, South Africa., Brackin R; Advanced Medical Bioimaging, Charité - Universitätsmedizin, 10-117 Berlin, Germany., Bouilhol E; Université de Bordeaux, Bordeaux Bioinformatics Center, 33000 Bordeaux, France.; Université de Bordeaux, CNRS, IBGC, UMR 5095, 33077 Bordeaux, France., Dartigues B; Université de Bordeaux, Bordeaux Bioinformatics Center, 33000 Bordeaux, France., Warrell JH; Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA., Pimentel MR; Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal., Beaume N; Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7295 Cape Town, South Africa., Fortunato IC; Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal., Dallongeville S; Unite D'Analyse D'Images Biologiques, Institut Pasteur, 75015 Paris, France., Boulle M; Chemogenomic and Biological Screening Core Facility, C2RT, Department of Structural Biology and Chemistry, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.; Université de Paris, Sorbonne Paris Cité, Paris, France., Soueidan H; Université de Bordeaux, Bordeaux Bioinformatics Center, 33000 Bordeaux, France., Agou F; Chemogenomic and Biological Screening Core Facility, C2RT, Department of Structural Biology and Chemistry, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.; Department of Structural Biology and Chemistry, URA 2185, Pasteur Institute, Paris, France., Schmoranzer J; Advanced Medical Bioimaging, Charité - Universitätsmedizin, 10-117 Berlin, Germany., Olivo-Marin JC; Unite D'Analyse D'Images Biologiques, Institut Pasteur, 75015 Paris, France., Franco CA; Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal., Gomes ER; Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal., Nikolski M; Université de Bordeaux, Bordeaux Bioinformatics Center, 33000 Bordeaux, France.; Université de Bordeaux, CNRS, IBGC, UMR 5095, 33077 Bordeaux, France., Mhlanga MM; Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.; Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, FNWI, Radboud University, 6525 GA Nijmegen, the Netherlands.; Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
Jazyk:	angličtina
Zdroj:	Cell reports methods [Cell Rep Methods] 2021 Sep 13; Vol. 1 (5), pp. 100068. Date of Electronic Publication: 2021 Sep 13 (Print Publication: 2021).
DOI:	10.1016/j.crmeth.2021.100068
Abstrakt:	Advances in single-cell RNA sequencing have allowed for the identification of cellular subtypes on the basis of quantification of the number of transcripts in each cell. However, cells might also differ in the spatial distribution of molecules, including RNAs. Here, we present DypFISH, an approach to quantitatively investigate the subcellular localization of RNA and protein. We introduce a range of analytical techniques to interrogate single-molecule RNA fluorescence in situ hybridization (smFISH) data in combination with protein immunolabeling. DypFISH is suited to study patterns of clustering of molecules, the association of mRNA-protein subcellular localization with microtubule organizing center orientation, and interdependence of mRNA-protein spatial distributions. We showcase how our analytical tools can achieve biological insights by utilizing cell micropatterning to constrain cellular architecture, which leads to reduction in subcellular mRNA distribution variation, allowing for the characterization of their localization patterns. Furthermore, we show that our method can be applied to physiological systems such as skeletal muscle fibers. Competing Interests: The authors declare no competing interests. (© 2022 The Authors.)
Databáze:	MEDLINE
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