A computational framework to study sub-cellular RNA localization

Aubin Samacoits, Racha Chouaib, Adham Safieddine, Abdel-Meneem Traboulsi, Wei Ouyang, Christophe Zimmer, Marion Peter, Edouard Bertrand (), Thomas Walter () and Florian Mueller ()
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Aubin Samacoits: Institut Pasteur and CNRS UMR 3691
Racha Chouaib: University of Montpellier, CNRS
Adham Safieddine: University of Montpellier, CNRS
Abdel-Meneem Traboulsi: University of Montpellier, CNRS
Wei Ouyang: Institut Pasteur and CNRS UMR 3691
Christophe Zimmer: Institut Pasteur and CNRS UMR 3691
Marion Peter: University of Montpellier, CNRS
Edouard Bertrand: University of Montpellier, CNRS
Thomas Walter: PSL-Research University, CBIO-Centre for Computational Biology
Florian Mueller: Institut Pasteur and CNRS UMR 3691

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: Abstract RNA localization is a crucial process for cellular function and can be quantitatively studied by single molecule FISH (smFISH). Here, we present an integrated analysis framework to analyze sub-cellular RNA localization. Using simulated images, we design and validate a set of features describing different RNA localization patterns including polarized distribution, accumulation in cell extensions or foci, at the cell membrane or nuclear envelope. These features are largely invariant to RNA levels, work in multiple cell lines, and can measure localization strength in perturbation experiments. Most importantly, they allow classification by supervised and unsupervised learning at unprecedented accuracy. We successfully validate our approach on representative experimental data. This analysis reveals a surprisingly high degree of localization heterogeneity at the single cell level, indicating a dynamic and plastic nature of RNA localization.

Date: 2018
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DOI: 10.1038/s41467-018-06868-w

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