Basal promoter

The DNA part of each control module can be divided into three main regions, the core or basal promoter elements, the promoter proximal elements and the distal enhancer elements (Figure 9.1). The best characterized core promoter element is the TATA box, a DNA sequence that is rich in A-T base pairs and located 25 base pairs upstream of the transcription start site. The TATA box is recognized by one of the basal transcription factors, the TATA box-binding protein, TBP, which is part of a multisubunit complex called TFIID. This complex in combination with RNA polymerase 11 and other basal transcription factors such as TFIIA and TFIIB form a preinitiation complex for transcription. 

Figure 9.1 The transcriptional elements of a eucaryotic structural gene extend over a large region of DNA. The regulatory sequences can be divided into three main regions (1) the basal promoter elements such as the TATA box, (2) the promoter proximal elements close to the initiation site, and (3) distal enhancer elements far from the initiation site.

Williams, G.T. Morimoto, R.I. (1990). Maximal stress-induced transcription from the human hsp70 promoter requires interactions with the basal promoter elements independent of rotational alignment. Mol. Cell. Biol. 10, 3125-3136. 

Edgar That is another great question that we don t know much about. All I can tell you is about that one experiment I mentioned in which a minigene with just a basal promoter can give low-level ubiquitous string expression and enough cell division to generate a fly. 

Zhang H, Roberts DN, Cairns BR (2005a) Genome-wide dynamics of Htzl, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell 123 219-231... 

With the help of proteins called transcription factors, RNA polymerase II recognizes and binds to the promoter region. The basal promoter region of eukaryotic genes usually has two consensus sequences called the TATA box (also called Hogness box) and the CAAT box. 

Enhancers may be brought close to the basal promoter region in space by bending of the DNA molecule (Figure 1-5-5). 

The ability of the enhancer to stimulate the promoter increased between the two-cell and four-cell stages. The fold stimulation following injection of a two-cell nucleus was about seven- to 20-fold (Figure 3). In contrast, cleavage of injected two-cell embryos to the four-cell stage that were then assayed for luciferase activity revealed a 20 to 100-fold stimulation in response to the enhancer. This increase was a consequence of both a two- to three-fold lower level of expression from the basal promoter in the four-cell embryo, as well as a two-fold increase in enhancer-driven expression when compared to the two-cell embryo (Henery et al., 1995). These results suggest that the role of the enhancer may be to relieve the repression that accompanies the formation of the two-cell embryo. This repression, however, was apparently absent in S phase-arrested embryos since the level of expression in these embryos was the same regardless of the presence or absence of the enhancer and. 

Eukaryotes have different RNA polymerase-binding promoter sequences than prokaryotes. The TATA consensus sequence of the eukaryotic promoter region is located 25 to 35 bp upstream from the transcription start site (Fig. 6.13). The low activity of basal promoters is greatly inaeased by the presence of other elements located upstream from the promoter called upstream regulatory elements. These elements are located 40 to 200 bp upstream of the promoter sequence and include the SP1 box, the CCAAT box, and the hormone response elements. Transcription from many eukaryotic promoters can be stimulated by control elements, called enhancers, located many thousands of base pairs away from the transcription start site and usually 100 to 200 bp in length. 

Promoter regions (switch on transcription) Upstream promoter sequence CAAT followed by Core (or Basal) promoter TATA (Hogness box) Sequence TTGACA (-35) followed by TATAAT (-10 or Pribnow box) are upstream of the transcription start (+1)... 

Williams GT, Morimoto RI (1990) Maximal stress-induced transcription from the human HSP70 promoter requires interactions with the basal promoter elements independent of rotational alignment. Mol Cell Biol 10 3125-3136 Willmann T, Beato M (1986) Steroid-free glucocorticoid receptor binds specifically to mouse mammary tumour virus DNA. Nature 324 688-691 Winkler H, Adam G, Mattes E, Schanz M, Hartig A, Ruis H (1988) Co-ordinate control of synthesis of mitochondrial and non-mitochondrial hemoproteins a binding site for the HAP-1 (CYPl) protein in the UAS region of the yeast catalase T gene. EMBO J 7 1799-1804... 

Finally, the third module is the basal promoter, which in this case binds the a -RNAP holoenzyme complex. This module is responsible for integrating all the inputs thereby generating a particular expression pattern at some integrated rate. The integration of the inputs takes place via a sequential kinetic mechanism, whereby the complex binds the promoter, but is unable to initiate expression, and as a result remains paused at the Transcriptional Start Site (TSS). Simultaneously, the rest of the transcription apparatus assembles at the various binding sites on the enhancer. Transcription is facilitated when the upstream assembled driver complex (e.g. NtrC - the driver (Amit et al. 2011)) loops and makes directs contact with the poised o -RNAP complex. The driver... 

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