Extended Figure 6. The transcription initiation pathway for SNR20* long (left panel) and SNR20* short promoters (right panel).

A model for the initiation pathway on the SNR20* long promoter. Left panel, with states starting from the top: Pol II (beige) with attached GTFs (blue) and ssl2 (orange) binds in its “closed” form to the promoter element upstream of the TSS (arrow) on the DNA template (green and blue lines). Positions of the enzyme active site (open white circle) and TATA box (closed black square) are indicated. Unwinding by TFIIH produces an open complex (OC) that leads to bubble formation. Arrival of the OC at the TSS due to scanning, driven by TFIIH, leads to the formation of an extended bubble (dashed lines indicate the speculative position of ssDNA. If the complex fails to recognize the TSS, it can be driven beyond it by TFIIH, resulting in a “fast state” that produces no RNA but advances at roughly twice the normal rate (black box; see text). When Pol II recognizes the TSS, it begins transcription of RNA (red line), corresponding to the initial transcription complex (ITC). Formation of the ITC leads to bubble collapse, followed by the loss of GTFs and transition to the elongation complex (EC). Corresponding model for the initiation pathway on the SNR20* short promoter. Right panel, with states starting from the top: Similar states as for SNR20* long. In this case, the OC does not need to scan for the TSS, which is found within its DNA footprint. As a consequence, the ITC can form and begin RNA synthesis once the active site has recognized the TSS. A longer segment of RNA can thereby be produced prior to the transition to the EC.