The RNA Polymerase II Core Promoter in Drosophila

Abstract

Transcription by RNA polymerase II initiates at the core promoter, which is sometimes referred to as the "gateway to transcription." Here, we describe the properties of the RNA polymerase II core promoter in Drosophila The core promoter is at a strategic position in the expression of genes, as it is the site of convergence of the signals that lead to transcriptional activation. Importantly, core promoters are diverse in terms of their structure and function. They are composed of various combinations of sequence motifs such as the TATA box, initiator (Inr), and downstream core promoter element (DPE). Different types of core promoters are transcribed via distinct mechanisms. Moreover, some transcriptional enhancers exhibit specificity for particular types of core promoters. These findings indicate that the core promoter is a central component of the transcriptional apparatus that regulates gene expression.

Keywords: FlyBook; RNA polymerase II; TBP; TBP-related factors; core promoter; core promoter elements; sequence-specific transcription factors.

Figure 1

The core promoter is a component of the transcriptional control region of a gene. The core promoter typically comprises the region from −40 to +40 relative to the +1 transcription start site (TSS), and contains the information that directs the initiation of transcription by RNA polymerase II. The core promoter functions with the proximal promoter and enhancer regions, both of which contain sites for the binding of sequence-specific DNA-binding transcription factors. The proximal promoter region spans from ∼ −40 to −250 relative to the TSS. Many genes contain multiple enhancers that are located at variable distances both upstream and downstream of the TSS.

Figure 2

Schematic diagram of some RNA polymerase II core promoter motif arrangements that are observed in Drosophila. The specific motifs are discussed in the text. In this figure, “Inr” refers to the consensus Inr as well as to an Inr-like sequence termed DMv4, and “TATA” refers to the consensus TATA box as well as to a TATA-like sequence termed DMv5. DMv4 and DMv5 are commonly observed in Drosophila core promoters (FitzGerald et al. 2006; Chen et al. 2014). This drawing is roughly to scale.

Figure 3

Analysis of chromatin structure at different types of core promoters suggests that promoters of regulated genes generally lack periodic arrays of nucleosomes. The diagrams are based on data from Rach et al. (2011). (A) Comparison of chromatin structure at focused vs. dispersed promoters. (B) Comparison of focused promoters that contain TATA, Inr, MTE, or DPE motifs vs. focused promoters that contain the TCT motif.

Figure 4

Postulated model for the role of sequence-specific DNA-binding transcription factors (ssTFs) in the initiation of transcription from promoters that lack core promoter motifs such as the TATA box and DPE. This model is discussed in the text.

Figure 5

Summary of our current knowledge of transcriptional programs that are carried out by TBP, TRF1, and TRF2 in Drosophila. The combined functions of Drosophila TBP and TRF1 are approximately the same as the functions of TBP in organisms, such as Saccharomyces cerevisiae, that contain only TBP. In contrast, TRF2 mediates new functions that are not present in organisms that lack TRFs.

Figure 6

Schematic diagram of enhancer-core promoter specificity, in which enhancers establish functional interactions with their cognate core promoters.