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 roles of the core promoter, downstream elements and chromatin structure in mediating regulation have been largely undefined. 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. Basal and activated transcription pathways recruit distinct transcription factor complexes to the core promoter elements and target distinct transcription initiation sites. Basal transcription is completely dependent upon the general transcription factor TAF1 whereas activated transcription initiates is TAF1 independent. To further characterize regulation of class I gene expression, we have undertaken to characterize core promoter elements in vivo and to identify novel downstream promoter elements. Surprisingly, introduction of mutations within the core promoter region do not markedly affect gene expression in vivo, indicating that no single core promoter element is necessary for transcription. Within 32 bp of translation initiation we have identified three additional, interacting elements that act in concert to achieve both positive and negative regulation of the upstream core promoter, both in vivo and in vitro. 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. While chromatin structure and remodeling play pivotal roles in the regulation of many inducible genes, this level of regulation has a much smaller role in class I expression. Thus, based on both ChIP analysis and nucleosomal mapping around the class I gene in various tissues, we find that the promoter is constitutively poised for expression, independent of the rate of transcription. Small changes in precise nucleosomal positioning are observed among the tissues that do correlate with level of expression. We hypothesize that the role of chromatin structure in regulating expression of constitutively expressed genes is distinct from that of inducible or tissue-restricted genes. In addition to the regulatory events occurring around the promoter, regulation is also mediated through a downstream boundary element which is necessary for sustained gene expression in vivo. Specifically, we have identified and characterized a boundary element within the intergenic region 3 of the class I gene. Using transgenic mice and stably transfected cell lines, we demonstrate that a 3 segment functions as a barrier element, protecting the MHC class I gene from silencing. Accordingly, truncation of the 3 sequences results in gene silencing, increased nucleosomes density and decreased histone H3K9 acetylation and H3K4 methylation across the gene. In addition, we show that histone modifying enzymes p300 and pCAF are associated with the 3 boundary element. Thus, dynamic and tissue-specific changes occur within the context of an open chromatin structure but depend upon a functional boundary element.
