H2A.Z and elongation factor Spt6 form an ancient bridge shaping transcription in eukaryotes

Abstract The chromatin fiber is thought to suppress transcription in eukaryotes by acting as a structural barrier. However, once begun, transcription can readily proceed on chromatin, suggesting this model is insufficient. Here, we establish that the ultra-conserved core domain of the ancestral histone H2A.Z dictates transcription elongation via direct interaction of its loop 2 region with the RNAPII subunit Spt6, rather than biophysical changes to chromatin. 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, driving either super-repressed or -activated transcriptional states. Our results place the histone core domain at the origin of eukaryotic gene expression, establishing its transformative power to shape transcription.