Section: New Results

Genome-wide search for factors that control the assembly of RNA granules

Participants : Wei Shen, Nicolas Cedilnik, Florence Besse, Xavier Descombes.

This work has been done in collaboration with Fabienne De Graeve from iBV

In vivo, mRNAs are packaged together with regulatory proteins into ribonucleoprotein particles (RNP) that control their fate and undergo extensive remodeling in response to developmental cues or environmental stresses. Cytoplasmic RNPs of different sizes, composition and regulatory properties have been described, including large macromolecular complexes such as P-bodies, stress granules, or germ cell granules. We aim at studying the different RNA granules distribution within the cytoplasm depending on genomic factors.

Before considering a spatial statistics analysis of the granules, it is necessary to detect them on confocal microscopy images of the cells. Therefore, we have studied a first pipeline for detecting these granules in confocal microscopy images. We have marked cells wih DAPI for detecting nuclei. These nuclei are then classified into "dead" or "alive" by a support vector machine (SVM) using intensity and shape criteria. In the second step we consider GFP marked images to segment the cytoplasm and detect the granules within the cytoplasm. The cytoplasm segmentation is performed using an active contour whereas the granule detection is based on a marked point process model optimized by the multiple births and cut algorithm.

The full pipeline has been validated on a few samples from a pilot study. The next step will consists of a validation on the full study before considering a genome-wide screening.

Figure 7. GFP-IMP particles are distinct from P-bodies. S2R+ cells expressing GFP-IMP fusions (left: green in the overlay) and stained with α-GW182 antibodies (middle: red in the overlay). GW182 is a well-described marker of P-bodies. Experiment performed in F. Besse lab at iBV (unpublished).