GSE115775
Spt6 is required for the fidelity of promoter selectivity
Spt6 is a conserved factor that controls transcription and chromatin structure across the genome. Although viewed as an elongation factor, spt6 mutations allow transcription from within coding regions, suggesting that Spt6 also controls initiation. To comprehensively characterize the requirement for Spt6 in transcription, we have used four approaches: TSS-seq and TFIIB ChIP-nexus to assay transcription initiation, NET-seq to assay elongating RNAPII, and MNase-seq to assay nucleosome occupancy and positioning. Our results demonstrate that Spt6 represses transcription initiation at thousands of intragenic promoters. We characterize these intragenic promoters, and find some features conserved with genic promoters and other features that are distinct. Finally, we show that Spt6 regulates transcription initiation at most genic promoters and propose a model of initiation site competition to account for this. Together, our results demonstrate that Spt6 controls the fidelity of transcription initiation throughout the genome and reveal the magnitude of the potential for expressing alternative genetic information via intragenic promoters. Overall design: Transcription start site sequencing for two replicates each of wild-type and spt6-1004 S. cerevisiae strains after an 80 minute shift from 30ºC to 37ºC. ChIP-nexus of TFIIB in two replicates each of wild-type and spt6-1004 strains after an 80 minute shift from 30ºC to 37ºC. Native elongating transcript sequencing of a wild-type strain after an 80 minute shift from 30ºC to 37ºC (two replicates), and spt6-1004 strains grown at 30ºC or shifted to 37ºC for 80 minutes (two replicates each). Two replicates of ChIP-nexus of Spt6 in a wild-type strain grown at 30ºC. Two replicates of ChIP-nexus of Rpb1 in a wild-type strain grown at 30ºC. MNase-sequencing of wild-type (one experiment) and spt6-1004 strains (two replicates) shifted from 30ºC to 37ºC for 80 minutes.