Transcription of major histocompatibility complex (MHC) class I genes is regulated by both tissue-specific (basal) and hormone/cytokine (activated) mechanisms. Although promoter-proximal regulatory elements have been characterized extensively, the role of the core promoter in mediating regulation has been largely undefined. We have found that the class I core promoter consists of distinct elements that are differentially utilized in basal and activated transcription pathways. These pathways recruit distinct transcription factor complexes to the core promoter elements and target distinct transcription initiation sites. Class I transcription initiates at four major sites within the core promoter and is clustered in two distinct regions: """"""""upstream"""""""" (-14 and -18) and """"""""downstream"""""""" (+12 and +1). Basal transcription initiates predominantly from the upstream start site region and is completely dependent upon the general transcription factor TAF1 (TAF(II)250). Activated transcription initiates predominantly from the downstream region and is TAF1 (TAF(II)250)independent. Both in vivo and in vitro, basal and activated transcriptions of an MHC class I gene target distinct core promoter domains, nucleate distinct transcription initiation complexes and initiate at distinct sites within the promoter. We have defined a novel core promoter feature that permits regulated transcription of the MHC class I gene, PD1, at the level of transcript start site (TSS) selection. The multiple, dispersed TSS encode a single protein, due to the absence of any ATG triplets within approximately 450 bp upstream of the authentic initiator ATG. Thus, the PD1 core promoter is embedded within an """"""""ATG desert"""""""". Remarkably, extending this analysis genome-wide, we find that ATG deserts occur non-randomly and most notably are associated with non-TATAA promoters, independent of the presence of CpG islands (CGIs). We further document a significant correlation between the use of multiple transcription start sites and non-TATAA promoters. We speculate that ATG deserts ensure that promoters with multiple TSS do not direct synthesis of aberrant protein products, thereby permitting them to serve as a platform to integrate complex upstream regulatory signals. We have proposed that transcription initiation at the core promoter is a dynamic process in which the mechanisms of core promoter function differ depending on the cellular environment.
