Most eukaryotic genes express mRNAs with alternative polyadenylation sites at 
their 3' ends. Here we show that polyadenylated 3' termini in three yeast 
species (Saccharomyces cerevisiae, Kluyveromyces lactis, and Debaryomyces 
hansenii) are remarkably heterogeneous. Instead of a few discrete 3' ends, the 
average yeast gene has an "end zone," a >200 bp window with >60 distinct poly(A) 
sites, the most used of which represents only 20% of the mRNA molecules. The 
pattern of polyadenylation within this zone varies across species, with D. 
hansenii possessing a higher focus on a single dominant point closer to the ORF 
terminus. Some polyadenylation occurs within mRNA coding regions with a strong 
bias toward the promoter. The polyadenylation pattern is determined by a highly 
degenerate sequence over a broad region and by a local sequence that relies on A 
residues after the cleavage point. Many dominant poly(A) sites are predicted to 
adopt a common secondary structure that may be recognized by the 
cleavage/polyadenylation machinery. We suggest that the end zone reflects a 
region permissive for polyadenylation, within which cleavage occurs 
preferentially at the A-rich sequence. In S. cerevisiae strains, D. hansenii 
genes adopt the S. cerevisiae polyadenylation profile, indicating that the 
polyadenylation pattern is mediated primarily by species-specific factors.