TF binding sites

TF binding site

Core Promoter

Proximal Promoter Region

Fig.7.1 Transcription control modules of a eukaryotic protein encoding-gene. Cis-acting DNA elements for an RNA

polymerase II transcribed gene are shown. The core promoter is recognized by the general transcriptional machinery, which includes RNA polymerase II. The start site of transcription maps to the core promoter and is indicated by the arrow. Enhancer and silencer elements, shown here upstream of the core promoter, contain binding sites for gene-specific regulatory factors that stimulate or repress mRNA synthesis. Insulators limit the distance over which enhancer and silencer sequences exert their stimulatory and inhibitory effects. The proximal promoter region encompasses the core promoter and proximal promoter elements that contain binding sites for other transcription factors (TF binding sites) that affect core promoter activity. The arrangement of these regulatory elements is commonly dispersed over a large region of genomic DNA and can extend both upstream and downstream of the core promoter.

Core Promoter

The core promoter was originally defined as the minimal length of contiguous DNA sufficient to support the accurate initiation of transcription in the absence of other cis-acting regulatory elements. The low level of activity detected in vitro from core promoters was termed basal transcription. Sequence analysis of eukaryotic core promoters has led to the identification of a number of prevalent DNA sequence motifs (Fig. 7.2). These core promoter elements are the TATA box, initiator (Inr), downstream promoter element (DPE), TFIIB recognition element (BRE), and motif ten element (MTE), each of which can be found in some but not all eukaryotic core promoter regions. The absence of a universal core promoter element has made it difficult to effectively map the transcriptional control modules for RNA polymerase II transcribed genes. The arrival of the genomic era will greatly aid the development of computational algorithms for predicting the core promoter region of a given gene.

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