A computational framework to study sub-cellular RNA localization

Aubin Samacoits (1, 2) , Racha Chouaib (3, 4) , Adham Safieddine (3, 4) , Abdel-Meneem Traboulsi (3, 4) , Christophe Zimmer (1, 2) , Wei Ouyang (1, 2) , Marion Peter (3, 4) , Edouard Bertrand (3, 4) , Thomas Walter (5, 6, 7) , Florian Mueller (1, 2)

1 Imagerie et Modélisation - Imaging and Modeling
2 C3BI - Centre de Bioinformatique, Biostatistique et Biologie Intégrative
3 IGMM - Institut de Génétique Moléculaire de Montpellier
4 Equipe labellisée Ligue contre le Cancer
5 CBIO - Centre de Bioinformatique
6 Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe
7 PSL - Université Paris sciences et lettres

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.

Domaines: Informatique [cs]; Bio-informatique [q-bio.QM]; Informatique [cs]; Vision par ordinateur et reconnaissance de formes [cs.CV]; Informatique [cs]; Traitement des images [eess.IV]; Sciences du Vivant [q-bio]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Aubin Samacoits, Racha Chouaib, Adham Safieddine, Abdel-Meneem Traboulsi, Christophe Zimmer, et al.. A computational framework to study sub-cellular RNA localization. Nature Communications, 2018, 9 (1), pp.4584. ⟨10.1038/s41467-018-06868-w⟩. ⟨hal-01984014⟩