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In molecular biology, a genetic reporter system (genetic reporter gene, reporter gene, reporter) is an assay in which a gene of interested is labeled with a particular gene sequence that allows for gene expression, regulation and cell signaling to be tracked and monitored. These gene sequences are usually located down stream of the regulatory sequence (promoter) of the gene of interest as a way of directly inferring transcriptional events that occur in the cell. Reporter genes are chosen by their ability to be detected and measured. A few examples include:


 * Fluorescent genes (gfp,rfp,yfp)
 * Luciferase
 * Chloramphenicol acetyltransferas e (CAT)
 * Alkaline phosphate (AP)
 * beta-galactosidase ($$\beta$$- gal)

Common reporter genes
 Fluorescent genes:  are genes that induce visually identifiable characteristics in the presence of an excitable wave length. Examples include green fluorescent protein (GFP), red fluorescent protein (RFP), and yellow fluorescent protein (YFP). These reporter genes have been employed in live cell models to study the development of certain organism (e.g. Murine, Human Embryonic Stem Cells and Induced Pluripotent Stem Cells) or the complexities of the structures within these organisms

 Luciferase:  the firefly luciferase enzyme is employed for its ability to detect ATP[2]

 Chloramphenicol acetyltransferase (CAT):  a bacterial enzyme that catalyzes the transfer of an acetyl group from acetyl-coenzymeA to Chloramphenicol [3]

 Alkaline phosphate (AP):  allows for the removal of phosphate monoesters which allow the prevention of self ligation. These enzymes usually carry chromogenic compounds like p-nitrophenyl phosphate (PNPP), flavin adenine dinucleotide phosphate (FADP) and chemiluminescent phenyl phosphate-substituted dioxetane (CSPD). [4].

$$\beta$$- galactosidase ($$\beta$$- gal): an enzyme that catalyzes the hydrolysis of galactosides into monosaccharides, used along with a synthetic chromogenic X-gal which allows for a blue product to be formed[5].

Introducing reporter genes
There are various methods of introducing reporter genes into a cell, commonly referred to as transformation for bacterial incorporation and transfection for eukaryotic. There are several methods including but not limited to calcium phosphate, DEAE-dextran, lipofection, and electroporation[6]. Introducing a reporter gene into an organism involves the ligation of a reporter gene and the gene of interest in the same DNA construct followed by insertion into the cell or organism. It is important to use a reporter gene that is not natively expressed in the cell or organism under study, since the expression of the reporter is being used as a marker for successful uptake of the gene of interest.

Reporter genes maybe expressed independently upon entry into the cell. Ubiquitous or specific promoter sequences upstream drive transcription or may be turned on with external interventions (e.g. Isopropyl β-D-1-thiogalactopyranoside (IPTG) in the β-galactosidase system). These systems usually have a short lifespan of about 24-72 hours, after which the reporter signal will gradually decline[6]. Another way of integrating a reporter gene that allows for prolonged and stable expression consists of integrating the nucleic acid sequence of the reporter gene into endogenous loci of the DNA. Hence the expression is dependent on the upstream promoter of the gene of interest. This technique is used throughout developmental biology, to understand cell origins and map cell fates. The efficiency of such method is quite low (0.001-1%), thus a selection method is often used to increase the likelihood of identifying a successful transformant[6].

Gene expression assays
Reporter genes can be employed to assay transcription, mRNA processing and translation of a particular gene. In these cases, the reporter is directly attached to the gene of interest to create a gene fusion. The two genes are under the same promoter elements and are transcribed into a single messenger RNA molecule. The mRNA is then translated into protein. In these cases it is important that both proteins be able to properly fold into their active conformations and interact with their substrates despite being fused. In building the DNA construct, a segment of DNA coding for a flexible polypeptide linker region is usually included such that the reporter and the gene product will only minimally interfere with one another. Reporter gene assay(s) have been increasingly used in high throughput screening (HTS) to identify small molecule inhibitors and activators of protein targets and pathways for drug discovery and chemical biology. Because the reporter enzymes themselves (e.g. firefly luciferase) can be direct targets of small molecules and confound the interpretation of HTS data, novel coincidence reporter designs incorporating artifact suppression have been developed [7][8]

Additionally, other polypeptide linkers have recently allowed for the separation of the reporter gene and gene of interest to exclude any interference that may occur with transcription (e.g.. 2A).

Promoter assays
Reporter genes can be used to assay for the activity of a particular promoter in a cell or organism (e.g.Chloramphenicol acetyltransferase).[9] In this case there is no separate "gene of interest"; the reporter gene is placed under the control of the target promoter and the reporter gene product's activity is quantitatively measured. Another example of this would be the luciferase reporter gene. The luciferase gene, coding for the luciferase enzyme, would be cloned upstream of the regulatory region of the gene of interest. The cloned construct would then be introduced into cells allowing for the regulatory elements to drive transcription of the luciferase gene. The products of the gene, specifically the luciferase enzyme, including all other proteins within the cell are collected for analysis. The analysis requires a specific reaction of luciferase, luciferin and other cofactors, which produce a light signal corresponding to transcription of the luciferase gene. The results are normally reported relative to the activity under a "consensus" promoter known to induce strong gene expression. The reporter signal is measured using a luminometer, which measures and quantifies the light emissions corresponding to the regulatory regions of the gene of interest.

Further uses
A more complex use of reporter genes on a large scale is in two-hybrid screening, which aims to identify proteins that natively interact with one another in vivo.