Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns

Recruitment of RNA polymerase II (Pol II) to promoter regions is essential for transcription. Despite conflicting evidence, the Pol II Pre-Initiation Complex (PIC) is often thought to be of uniform composition and assemble at all promoters via an identical mechanism. Here, we show using Drosophila melanogaster S2 cells as a model that promoter classes with distinct functions and initiation patterns function via PICs that display different compositions and dependencies: developmental promoter DNA readily associates with the canonical Pol II PIC, whereas housekeeping promoter DNA does not and instead recruit different factors such as DREF. Consistently, TBP and DREF are required by distinct sets of promoters, and TBP and its paralog TRF2 function at different promoter types, partly exclusively and partly redundantly. In contrast, TFIIA is required for transcription from all promoters, and we identify factors that can recruit and/or stabilize TFIIA at housekeeping promoters and activate transcription. We show that promoter activation by these factors is sufficient to induce the dispersed transcription initiation patterns characteristic of housekeeping promoters. Thus, different promoter classes direct distinct mechanisms of transcription initiation, which relate to different focused versus dispersed initiation patterns.