Yeast Upf Proteins Required for RNA Surveillance Affect Global Expression of the Yeast Transcriptome

Abstract

mRNAs are monitored for errors in gene expression by RNA surveillance, in which mRNAs that cannot be fully translated are degraded by the nonsense-mediated mRNA decay pathway (NMD). RNA surveillance ensures that potentially deleterious truncated proteins are seldom made. NMD pathways that promote surveillance have been found in a wide range of eukaryotes. In Saccharomyces cerevisiae, the proteins encoded by the UPF1, UPF2, and UPF3 genes catalyze steps in NMD and are required for RNA surveillance. In this report, we show that the Upf proteins are also required to control the total accumulation of a large number of mRNAs in addition to their role in RNA surveillance. High-density oligonucleotide arrays were used to monitor global changes in the yeast transcriptome caused by loss of UPF gene function. Null mutations in the UPF genes caused altered accumulation of hundreds of mRNAs. The majority were increased in abundance, but some were decreased. The same mRNAs were affected regardless of which of the three UPF gene was inactivated. The proteins encoded by UPF-dependent mRNAs were broadly distributed by function but were underrepresented in two MIPS (Munich Information Center for Protein Sequences) categories: protein synthesis and protein destination. In a UPF⁺ strain, the average level of expression of UPF-dependent mRNAs was threefold lower than the average level of expression of all mRNAs in the transcriptome, suggesting that highly abundant mRNAs were underrepresented. We suggest a model for how the abundance of hundreds of mRNAs might be controlled by the Upf proteins.

ACKNOWLEDGMENTS

We are indebted to members of the Affymetrix Academic User’s Center, notably Chris Harrington and Sumathi Venkatapathy, for valuable technical expertise. We thank Renee Shirley, Amanda Ford, and Judith Berman for critical reading of the manuscript and Jeff Dahlsied and Erin O’Shea for helpful discussions.

Microarray analysis was performed by M.J.L. at the Affymetrix Academic User’s Center, which is funded by NIH grant PO1 HG01323. The research was supported by the College of Agricultural and Life Sciences, University of Wisconsin, Madison, under NSF grant MCB-9870313 (M.R.C.). M.J.L. was supported by NRSA postdoctoral fellowship NIH GM19070. Additional funding was provided by the Research Committee of the University of Wisconsin Medical School.