The RNA Polymerase II Core Promoter

Abstract

The events leading to transcription of eukaryotic protein-coding genes culminate in the positioning of RNA polymerase II at the correct initiation site. The core promoter, which can extend ~35 bp upstream and/or downstream of this site, plays a central role in regulating initiation. Specific DNA elements within the core promoter bind the factors that nucleate the assembly of a functional preinitiation complex and integrate stimulatory and repressive signals from factors bound at distal sites. Although core promoter structure was originally thought to be invariant, a remarkable degree of diversity has become apparent. This article reviews the structural and functional diversity of the RNA polymerase II core promoter.

Promoter architectures and developmental gene regulation

“…1). Assembly of a PIC at such promoters is initiated by TFIID binding to the TATA-box, Inr sequence and/or other sites [2]. TFIID is a multi-protein complex comprising the TATA-box binding protein (TBP) and more than 10 distinct TBP-associated factors (TAFs) [1].…”

“…The consensus sequences of Drosophila and vertebrate Inr differ to some extent (Fig. 1), however in both cases they are bound by the homologous TAFs within the TFIID complex, which include TAF1 and TAF2 [2]. The common characteristic of the Inr element is the pyrimidine (C or T) / purine (A or G) motif (i.e.…”

“…The common characteristic of the Inr element is the pyrimidine (C or T) / purine (A or G) motif (i.e. YR) positioned -1/+1 bp relative to the TSS, so that the purine is the first transcribed nucleotide [2,12]. Inr element often occurs in combination with either TATA-box [71], or with another core promoter element located downstream of the TSS, the downstream promoter element (DPE) [72].…”

Molecular and Genetic Characterization of a Taf1p Domain Essential for Yeast TFIID Assembly

“…On promoters containing a TATA box, Tafps help stabilize TBP binding to the TATA element via interaction with TATA-proximal initiator DNA sequences (69). Tafp-DNA interactions may be particularly important for TFIID binding to promoters that lack a canonical TATA element and contain TATA-proximal initiator and distal promoter element sequences (13,15,42,69,76). Second, Tafps can function as coactivators during transcriptional activation by making direct contacts with specific activators leading to an increase in PolII PIC formation (1, 16).…”

“…First, TFIID functions during promoter recognition by binding directly to the promoter (67,76,77). On promoters containing a TATA box, Tafps help stabilize TBP binding to the TATA element via interaction with TATA-proximal initiator DNA sequences (69). Tafp-DNA interactions may be particularly important for TFIID binding to promoters that lack a canonical TATA element and contain TATA-proximal initiator and distal promoter element sequences (13,15,42,69,76).…”