Single residues in the histone core domain guide transcription

The nucleosome is thought to suppress transcription in eukaryotes by acting as a structural barrier. However, once begun, transcription can readily proceed in the presence of nucleosomes, suggesting this model is insufficient. Here, we establish that the ultra-conserved core domain of the ancestral histone H2A.Z informs transcription elongation via direct interaction of its loop 2 region with the transcription elongation factor Spt6. Interrogating H2A.Z sequences representing more than a billion years of eukaryotic evolution in a single synthetic host, we show that Spt6 can distinguish even single-residue substitutions within their loop 2, controlling RNAPII processivity. Our results place the histone core domain at the origin of eukaryotic gene expression, establishing it as a powerful force shaping transcription. Overall design: To investigate the effect H2A.Z mutants on Spt6 chromatin localization more precisely, a series of S. pombe lines wherein the endogenous gene (Pht1) was mutated using standard approaches, and then ChIP-seq on myc-tagged Spt6 was performed.