In yeast, the accelerated rate of decay of nonsense mutant mRNAs, called nonsense-mediated mRNA decay, requires three proteins, Upf1p, Upf2p, and Upf3p. Single, double, and triple disruptions of the UPF genes had nearly identical effects on nonsense mRNA accumulation, suggesting that the encoded proteins function in a common pathway. We examined the distribution of epitope-tagged versions of Upf proteins by sucrose density gradient fractionation of soluble lysates and found that all three proteins co-distributed with 80 S ribosomal particles and polyribosomes. Treatment of lysates with RNase A caused a coincident collapse of polyribosomes and each Upf protein into fractions containing 80 S ribosomal particles, as expected for proteins that are associated with polyribosomes. Mutations in the cysteine-rich (zinc finger) and RNA helicase domains of Upf1p caused loss of function, but the mutant proteins remained polyribosome-associated. Density gradient profiles for Upf1p were unchanged in the absence of Upf3p, and although similar, were modestly shifted to fractions lighter than those containing polyribosomes in the absence of Upf2p. Upf2p shifted toward heavier polyribosome fractions in the absence of Upf1p and into fractions containing 80 S particles and lighter fractions in the absence of Upf3p. Our results suggest that the association of Upf2p with polyribosomes typically found in a wild-type strain depends on the presence and opposing effects of Upf1p and Upf3p.The notion of a global pathway for eukaryotic mRNA decay suggested by early work in animal cells has recently been greatly advanced by studies in the yeast Saccharomyces cerevisiae (1-4). Using an in vivo transcriptional pulse, the temporal fate of newly synthesized mRNA was established by monitoring poly(A) tail length, loss of the m 7 Gppp cap, disappearance of the mRNA, and the appearance of degradation intermediates. mRNAs with shorter half-lives were generally subject to faster rates of deadenylation and decapping. Once the poly(A) tails were reduced to a short oligo(A) length (10 -12 nucleotides), the mRNAs were decapped and digested from the 5Ј end. Decapping requires Dcp1p (5). Processive degradation from the 5Ј end requires the product of the XRN1 gene, which is known to encode a 5Ј 3 3Ј exoribonuclease (6). Deadenylation-dependent decapping followed by 5Ј 3 3Ј exonucleolytic decay is likely to be the global default pathway for the degradation of most eukaryotic mRNAs.Yeast mRNAs containing a premature stop codon decay more rapidly than their wild-type counterparts (7). This accelerated decay, called nonsense-mediated mRNA decay (NMD), 1 requires cis-acting elements in the mRNA in addition to a premature stop codon (8). Premature translational termination triggers decapping at the 5Ј end of nonsense mRNAs with kinetics that are independent of deadenylation (9). Following decapping, decay proceeds through the Xrn1p-mediated nucleolysis that is common to intrinsic decay. These results support the view that when translation is prematurely terminat...