Gcn4 motif binding in vivo correlates with binding in vitro and with gene induction levels. (A) Correlation between Gcn4 binding in vivo and in vitro for all AP-1 motifs (black circles, RY motifs; blue circles, RR/YY motifs; red circles, YR motifs). A log–log plot was used to decompress the data (values of R are for linear data). (B) AP-1 motifs located in ORFs. (C) AP-1 motifs located in promoters (defined as located within 600 bp upstream of the transcription start site [TSS] unless present in an ORF). (D) RY motifs in ORFs and promoters are occupied at similar levels in vitro (G-SELEX data). (E) Gcn4 binds to RY motifs in promoters at higher levels than to RY motifs in ORFs (ChIP-seq data for induced and uninduced wild-type cells and for induced gcn4Δ cells). (F) Gcn4 motif binding in vivo (induced wild-type cells) correlates with gene induction (defined by the ratio of bound Pol II [Rpb3 subunit] in induced and uninduced cells measured by ChIP-seq), whereas Gcn4 binding at promoter sites in vitro correlates with induction ratio, but Gcn4 binding at ORF sites does not.