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The Bur1–Bur2 and Paf1 complexes function during transcription elongation and affect histone modifications. Here we describe new roles for Bur1–Bur2 and the Paf1 complex. We find that histone H3 K36 tri‐methylation requires specific components of the Paf1 complex and that K36 tri‐methylation is more strongly affected at the 5′ ends of genes in paf1Δ and bur2Δ strains in parallel with increased acetylation of histones H3 and H4. Interestingly, the 5′ increase in histone acetylation is independent of K36 methylation, and therefore is mechanistically distinct from the methylation‐driven deacetylation that occurs at the 3′ ends of genes. Finally, Bur1–Bur2 and the Paf1 complex have a second methylation‐independent function, since bur2Δ set2Δ and paf1Δ set2Δ double mutants display enhanced histone acetylation at the 3′ ends of genes and increased cryptic transcription initiation. These findings identify new …