Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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A Genetic Interaction Map of RNA Processing Factors Reveals Links Between mRNA Processing Complexes

ABSTRACT: All classes of RNA undergo processing. The two largest RNA processing complexes are those involved in rRNA biogenesis and mRNA splicing. Because of their complexity and essential roles, it has been difficult to dissect the functional interactions within these machines as well as to identify possible cross-talk with other steps in gene expression. Here we report the results of a high-density, quantitative genetic interaction map comprising 107,155 individual interactions involving 552 mutants, 166 of which are hypomorphic alleles of essential genes (This data is available at The Krogan Lab Interactome Database). Our data allow unique insights into the functional organization of the RNA processing machines. For example, we identify unexpected connections involving a component of the 19S proteasome, Sem1/Dss1. We show that Sem1 has genetic, physical and functional interactions with the mRNA export complex, Thp1-Sac3; it also interacts physically with a putative component of the COP9 signalosome, Csn12. We show using splicing-specific microarrays that Csn12 has an unanticipated role in mRNA splicing. Finally, we demonstrate the utility of this dataset in determining functions for uncharacterized ORFs. We show that deletion of the uncharacterized YNR004W causes a very similar splicing defect to that caused by deletion of TGS1, the enzyme that trimethylates the caps of snRNAs and snoRNAs. Keywords: E-MAP, RNA Processing, splicing, splicing-specific microarray, CSN12, COP9 signalosome Splicing-specific microarrays were used to assay the changes to splicing caused by deletion of several non-essential genes which had no previously characterized role in mRNA splicing but were suggested to be involved in this process by high-throughput genetic and/or protein-protein interaction data in Saccharomyces cerevisiae. The data includes samples collected from some mutants in log phase growth at 30 degrees C and from some mutants shifted to 16 degrees C, all competitively hybridized against wild type samples collected under the same conditions. .

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Megan Bergkessel

PROVIDER: E-GEOD-11634 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.

Wilmes Gwendolyn M GM Bergkessel Megan M Bandyopadhyay Sourav S Shales Michael M Braberg Hannes H Cagney Gerard G Collins Sean R SR Whitworth Gregg B GB Kress Tracy L TL Weissman Jonathan S JS Ideker Trey T Guthrie Christine C Krogan Nevan J NJ

Molecular cell 20081201 5

We used a quantitative, high-density genetic interaction map, or E-MAP (Epistatic MiniArray Profile), to interrogate the relationships within and between RNA-processing pathways. Due to their complexity and the essential roles of many of the components, these pathways have been difficult to functionally dissect. Here, we report the results for 107,155 individual interactions involving 552 mutations, 166 of which are hypomorphic alleles of essential genes. Our data enabled the discovery of links ...[more]

PMID: 19061648

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Dataset Information

A Genetic Interaction Map of RNA Processing Factors Reveals Links Between mRNA Processing Complexes

Publications

A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.

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