Genetic analysis of polyadenylation patterns reveals distinct classes of yeast genes and local chromatin effects on Pol II elongation

The poly(A) profile of a typical yeast gene comprises ∼50 poly(A) sites corresponding to distinct 3' mRNA isoforms. Poly(A) profiles are shifted upstream in strains with slow RNA polymerase II (Pol II) elongation rates resulting from Pol II mutations or from depletion of histone chaperones FACT or Spt6. Conversely, downstream-shifted poly(A) profiles occur in strains with fast Pol II elongation rates caused by Pol II mutations or by depletion of histones. Downstream-shifted poly(A) profiles also arise when components of the cleavage/polyadenylation machinery are depleted. Here we examine poly(A) profiles in 45 yeast strains with mutations that affect a wide variety of DNA- or RNA-based processes. Typically, altered poly(A) profiles occur in only a subset of genes, and some strains show both upstream and downstream poly(A) shifts depending on the gene. Hierarchical clustering of the poly(A) profiles reveals 6 classes of genes that behave similarly over the genetic conditions tested and have different RNA sequence preferences in their 3' untranslated regions. Many chromatin-modifying or chromatin-associated proteins affect poly(A) profiles similarly to Pol II elongation rate mutants, indicating that they affect the rate of transcriptional elongation. Chromatin-modifying activities, but not cleavage/polyadenylation factors, often have non-uniform effects on 3' mRNA isoform levels of the same gene, suggesting that chromatin differentially affects Pol II dwell time at individual sites during transcriptional elongation.