Promoter deletion analysis

The promoter deletion analysis data and the CHX data are summarised in a model of the PR-la promoter shown in Fig. 5. The promoter appears to have a complex architecture comprising several cw-acting domains... 

The methods used for the evaluation of regulation of gene expression are too numerous to be described in detail here. They include Northern analysis to determine levels of a particular mRNA, nuclear run on to determine whether an increase in mRNA is due to an increase in the rate of transcription, and promoter deletion analysis to identify specific elements in the promoter region responsible for the control of expression. Of much current interest is the use of microarrays that permit the study of the expression of hundreds to thousands of genes at the same time. Reverse transcriptase-polymerase chain reaction and RNase protection assay techniques are used to amplify and quantitate mRNAs, while the electrophoretic mobility shift assay is used to measure binding of a transcription factor to its specific DNA consensus sequence. 

Promoter Deletion Analysis/Reporter Gene Assays... 

Figure 2.9. Luciferase reporter gene assay/promoter deletion analysis. Cells are transfected with the CYP1A1 promoter reporter (luciferase) constructs in which the promoter region is increasing deleted. The cells are then treated with benzo[a]pyrene (an inducer of CYP1A1), and cells are harvested 24-48hr later and luciferase activity is measured. Promoter deletion analysis revealed enhancer element between -1140 and -1029. Contained within this region is xenobiotic response element (XRE) to which the aryl hydrocarbon receptor (AHR) binds.

Wang, J. Oard, J.H. Rice ubiquitin promoters deletion analysis and potential usefulness in plant transformation systems. Plant Cell Rep. 2003, 22 (2), 129-134. 

A combination of promoter deletion analysis, linker scanning, site-directed mutagenesis, gain-of-function analysis, gel mobility shift assays, DNA methylation interference and DNase 1 footprinting have been used to search for AuxREs within auxin-responsive promoters. Two types of AuxREs have been identified using these experimental approaches. One of these is the ocs or as-1 element and the other is theTGTCNC element (discussed in Section 4.3.). 

To analyze structure/function relationship of different elements within the GRR, we studied the function of different deletion and point mutants. The human pi05 GRR contains 19 Gly residues (out of 29 residues in total 376-GGGSGAGAGGGGMFGSGGGGGGTGSTGPG-404), two of which are interspaced by Ala (380-GAGAG-384). Deletion analysis revealed that only 6 (382-GAGGGGMFGS-391) Gly residues are sufficient to promote, at least partially, generation of p50. Importantly, the Ala residue is essential (16). 

The promoter is necessary for expression of the lac operon and is thought to be the site for the initiation of RNA transcription. The site of the promoter cannot lie in the operator or structural genes, since mutations localized to the operator region do not lower or abolish the rate of synthesis of the enzymes, and deletion of the early portions of the z gene does not necessarily affect the rate of synthesis of the permease or transacetylase. The location of the promoter determined by deletion analysis is adjacent to the operator on the side away from the structural genes [22]. 

The effects of hypoxia on TH promoter activity in PC 12 cells have been studied by deletion analysis and transient expression of various TH promoter-... 

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