Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5′ Promoters in Yeast

Yashpal Rawal, Răzvan V. Chereji, Vishalini Valabhoju, Hongfang Qiu, Josefina Ocampo, David J. Clark, Alan G. Hinnebusch

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


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 ∼30% of Gcn4-binding motifs. Surprisingly, only ∼40% of the bound sites are in promoters, of which only ∼60% activate transcription, indicating extensive negative control over Gcn4 function. Most of the remaining ∼300 Gcn4-bound sites are within coding sequences (CDSs), with ∼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. Rawal et al. showed that the yeast transcription factor Gcn4 frequently binds within nucleosome-occupied protein coding regions in yeast cells and that a substantial fraction of these events confer activation of cryptic internal promoters as well as canonical 5′-positioned promoters at the same or adjacent genes.

Original languageEnglish (US)
Pages (from-to)297-311.e4
JournalMolecular Cell
Issue number2
StatePublished - Apr 19 2018
Externally publishedYes


  • activation
  • cryptic promoters
  • Gcn4
  • nucleosomes
  • transcription

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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