Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 50 Promoters in Yeast

Gcn4 is a yeast transcriptional activator induced by amino acid starvation. ChIP-seq analysis revealed 546 genomic sites occupied by Gcn4 in starved cells, representing similar to 30% of Gcn4-binding motifs. Surprisingly, only similar to 40% of the bound sites are in promoters, of which only similar to 60% activate transcription, indicating extensive negative control over Gcn4 function. Most of the remaining similar to 300 Gcn4-bound sites are within coding sequences (CDSs), with similar to 75 representing the only bound sites near Gcn4-induced genes. Many such unconventional sites map between divergent antisense and sub-genic sense transcripts induced within CDSs adjacent to induced TBP peaks, consistent with Gcn4 activation of cryptic bidirectional internal promoters. Mutational analysis confirms that Gcn4 sites within CDSs can activate sub-genic and full-length transcripts from the same or adjacent genes, showing that functional Gcn4 binding is not confined to promoters. Our results show that internal promoters can be regulated by an activator that functions at conventional 5'-positioned promoters.