UCSF

Cells must respond to a wide range of external stimuli by altering their gene expression programs. The contribution to these responses of changes to transcription initiation has been studied extensively, but subsequent mRNA processing steps can also be regulated. In this work, we have investigated the potential for regulation at the level of pre-mRNA splicing. We found that the pre-mRNAs for a majority of the ribosomal protein genes (RPGs) rapidly accumulated in response to amino acid starvation. By contrast, most RPG pre-mRNAs were rapidly degraded by the nuclear exosome in response to a variety of stresses that inactivated TORC1. These responses required casein kinase 2. In the case of amino acid starvation, the native promoter of an RPG, but not its native intron, was also required for the response. This suggested that the mechanism of splicing inhibition following amino acid starvation involved modulation of the co-transcriptional dynamics of spliceosome recruitment. Consistent with this model, we found that the inhibition of pre-mRNA splicing was accompanied by a rapid accumulation of both U1 snRNP and RNA polymerase II at the 3' ends of many ribosomal protein genes, suggesting that U1 release was inhibited. This inhibition of U1 release was insufficient to fully commit the RPG pre-mRNAs to eventual splicing however, as single molecule RNA FISH revealed that the accumulating pre-mRNAs localized to the cytoplasm during amino acid starvation. These results suggested a high degree of interaction among transcription, splicing, 3' end processing, and mRNA export, and we carried out a high throughput genetic screen to identify interactions among factors and complexes involved in mRNA processing. This screen revealed previously unknown connections between a proteasome component (Sem1) and mRNA export, and between a component of the COP9 signalosome and pre-mRNA splicing. We hope this dataset will also continue to be useful as we and others continue efforts to elucidate the interconnected regulatory mechanisms that contribute to control of gene expression at the level of mRNA processing.