Genome-wide function of Processing Bodies in mRNA decay

Translation and mRNA degradation are intertwined and critical aspects of post-transcriptional control. A conserved component of the mRNA decapping machinery is Edc3, which binds the decapping enzyme and can enhance its activity, and plays an important role in the assembly of P-bodies. Despite these roles, Edc3 is thought to only directly affect the decay rates of two yeast mRNAs. By analysis of the transcriptome in edc3Δ strains we demonstrate that Edc3 modulates the levels and decay rates of hundreds of yeast mRNAs by both promoting and inhibiting decapping in a transcript and growth condition specific manner. Moreover, accelerated decapping of specific mRNAs in edc3Δ strains is promoted by the mRNP aggregation driven by the Lsm4 protein. These results demonstrate that Edc3 is a multifunctional protein with both positive and negative effects of decapping and that aggregation of mRNPs into larger complexes can influence the rate of decapping.