The Basal Transcriptional Machinery

In this chapter, we will discuss the precise spaciotemporal formation of the basal transcriptional machinery on TSS regions, which are also known as core promoters. This is a prerequisite for understanding how transcription by Pol II is controlled. Pol II is the core of the basal transcriptional machinery that contains a large number of general transcription factors (GTFs), such as the TATA box-binding protein (TBP), many of which are summarized as the transcription factor (TF) IID complex. The TATA box is the prototype of a site-specific TFBS determining the position of Pol II on the TSS. However, genome-wide analysis showed that the majority of human genes use alternative binding sites for GTFs. Diversity and complexity of the human transcriptome are based on that most genes have multiple TSS regions and that the TSS of many genes is not a single defined nucleotide. The basal transcriptional machinery interacts via another multiprotein complex of coactivators, termed the MED complex, with a large variation of transcription factors. In parallel, the MED complex coordinates the action of cofactors of transcription factors, some of which are chromatin modifying enzymes.