Compartmentation and intracellular traffic of mRNPs

In eukaryotic cells, cytoplasmic mRNAs can be translated, degraded or stored, depending on the proteins which are bound to them. This post-transcriptional regulation is important for all aspects of cell physiology, in both germline and somatic cells.

Remarkably, most implicated factors accumulate in cytoplasmic membrane-less ribonucleoprotein (RNP) granules. In spite of different names, size and exact composition, depending on the model organism, the cell type and the environmental conditions, the common feature of these granules is that they contain repressed mRNAs. In the absence of any purification protocol which would enable to identify all their protein and RNA components, their function remains enigmatic. How do they assemble? Do they contain all repressed mRNAs or only a subpopulation? What is the advantage of these macro-aggregates compared to dispersed mRNPs? We tackle these questions using a combination of experimental approaches including biochemical and cell imaging techniques, as well as proteomic and transcriptomic analyses. Most our studies focus on P-bodies in human cells and germ granules in C. elegans. 

Highlights

Having previously shown that the DEAD-box helicase DDX6 is required for the assembly of P-bodies in human cells, we focused our studies on this protein. In vitro, we found that DDX6 binds RNA with high affinity and no sequence specificity, leading to RNA unfolding. In cells, DDX6 is a very abundant protein, seven-fold more than mRNA molecules. It multimerizes along repressed mRNAs. In electron microscopy, DDX6 is highly concentrated in P-bodies, where it decorates fibers which likely correspond to repressed RNAs. Studies in various model organisms have shown that DDX6 is a component of various complexes, including the decapping complex and translation repression complexes. In human cells, we have identified more than 200 protein partners, using the TAP-tag technique coupled to mass spectrometry analysis. The most abundant partners are proteins of the decapping complex, a CPEB-like complex and a poorly characterized ATXN2/2L complex. Only the decapping and the CPEB-like complexes are present in P-bodies, and only two proteins of the CPEB-like complex, 4E-T and LSM14A, are required with DDX6 to assemble P-bodies. These results suggest that the function of P-bodies is directly related to translation repression rather than to mRNA degradation.

Future directions

After obtaining this extended view of DDX6 interactome in human cells, we now want to identify which mRNA are regulated by DDX6, and by which mechanism, mRNA decay or translation repression. First, we are using a reporter assay enabling the artificial binding of DDX6 to a reporter mRNA (tether assay). Second, we conducted a polysome profiling experiment after DDX6 silencing with siRNAs. This strategy provides us with a genome-wide landscape of all regulation pathways involving DDX6, whether acting on mRNA decay or translation. Besides, we have set up the first efficient protocol of P-body purification, which will enable us to identify all its protein and RNA components. We hope that this will lead to major progress in the understanding of RNP granule functions. Finally, we study the function of RNP granules in the C. elegans model. Germ granules are regulated upon oocyte differentiation, and become very large in quiescent oocytes. Using mutants which do not form granules or form abnormal granules, we can question the function of these granules in the storage of maternal mRNAs and in the fitness of resulting embryos.

Collaborations

  • Philippe Andrey: INRA-AgroParisTech, Versailles-Grignon, France
  • Thomas Boudier: UPMC, Paris, France
  •  Eric Deprez: ENS Cachan, France
  • Eric Le Cam: Institut Gustave Roussy, Villejuif, France
  • Julien Mozziconacci: LPTMC, UPMC, Paris, France
  • Gérard Pierron: Institut Gustave Roussy, Villejuif, France
  •  Raquel Seruca: IPATIMUP, University of Porto, Portugal
  • Nancy Standart: Dept of Biochemistry, University of Cambridge, UK