Supplemental Methods

Reference points TFIIB (Sua7, PEGR ID 12275) locations defined by ChExMix (Yamada et al., 2020) were used as PIC reference points (Rossi et al., 2021; Supplemental Table S1, column G). The Sua7 ChExMix peaks were associated with the closest annotated TSS (Rossi et al. 2021; Xu et al., 2009; Supplemental Table S1, column H) and then the set was filtered to retain the closest Sua7 peak within a -100 to +61 bp window around the TSS. These limits were intended to accommodate variance in annotated PIC and TSS locations while minimizing capture of adjacent PICs. Due to Pol II scanning, a TSS does not always align with a PIC. Therefore, Sua7 peaks were preferred over annotated TSSs. If more than one TSS was associated with the same Sua7 peak, then only the TSS closest to the Sua7 peak was assigned. For all remaining genes without an assigned Sua7 ChExMix peak, the Sua7 annotation defaulted to the TSS annotation. For targets that were enriched at the +1 nucleosome, the +1 nucleosome dyad defined by H3/H4 MNaseseq (Rossi et al. 2021) was used as a reference point (Supplemental Table S1, column I). For targets that bound to the UAS region, the UAS as defined by (Rossi et al., 2021) was used (Supplemental Table S1, column E). In promoter cases where a UAS was not identified, we instead used a distance that was 150 bp upstream (more 5’) of the TSS location (Supplemental Table S1, column D). This distance was based on the average distance that SAGA (Spt7, PEGR ID 11960) ChIP-exo peaks were located upstream of a TSS location.