The initiation of messenger RNA synthesis by RNA polymerase II is regulated by a collection of cis-acting DNA elements. The core promoter, which is typically found -40 bp upstream and downstream of the transcription start site, plays a crucial role in the recruitment and positioning of the basic transcription machinery. DNA elements within the core promoter can also control the levels of gene transcription and specify enhancer selectivity. These regulatory functions are consistent with the large degree of diversity that has become apparent within core promoters. In this article, we will discuss our current understanding of the structure and function of core promoter elements in the regulation of transcription by RNA polymerase II.


The synthesis of messenger RNA (mRNA) from eukaryotic protein encoding genes, a process known as transcription, is essential for all biological processes including cell proliferation, differentiation, and survival. Transcription is carried out by RNA polymerase II and a set of general transcription factors (for review see Orphanides et al., 1996). The ability of these proteins to support mRNA synthesis is subject to regulation by cis-acting DNA elements. These DNA elements can be found both upstream and downstream of the transcription start site of a gene. They serve as recognition sites for proteins that facilitate or hinder the recruitment, binding and/or assembly of the transcription apparatus. There are distinct types of transcription control modules for RNA polymerase II transcribed genes, including enhancers, silencers, proximal promoter elements, the core promoter, and boundary/insulator elements. A schematic diagram of the transcription control modules of a typical eukaryotic protein encoding gene is provided in Fig.7.1.

Enhancers and silencers are distal control elements that can be located many thousands of base pairs away from the transcription start site (designated +1) and activate or repress transcription respectively (Bondarenko et al., 2003; Ogbourne and Antalis, 1998). A unique feature of enhancer elements is their ability to function in a position and orientation independent manner. Boundary/insulator sequences limit the domain within the genome at which enhancers and silencers exert their effect (Kuhn and Geyer, 2003). The core promoter, typically restricted to a region centered on the transcription start site, is where the transcription apparatus is assembled and the site of RNA polymerase II action. DNA sequences located near the immediate vicinity of the core promoter (from approximately -250 to +250) are often referred to as proximal promoter elements. Proximal promoter elements sometimes are considered part of a gene's promoter and include binding sites for trans-acting factors that affect transcription levels. The structure and function of cis-acting DNA elements within the core promoter will be the focus of

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this article.

Distal Enhancer


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