Transcription Factor Binding Site: Prediction & Concept

Instructor: Shannon Compton

Shannon teaches Microbiology and has a Master's and a PhD in Biomedical Science. She also researches cancer and neurodegenerative diseases.

What is a transcription factor binding site? What is the purpose of a transcription factor binding site? Why are these sites important to regulating gene expression? These questions will be addressed in this lesson.

What is a Transcription Factor Binding Site?

To begin, we need to define a transcription factor (TF). A TF is a protein that can bind to DNA and regulate gene expression. The region of the gene to which TF binds is called a transcription factor binding site. These sites are a subset of DNA binding sites. Overall, these sites can be defined as short segments of DNA that are specifically bound by one or more proteins with various functions. If you think about a parking lot with assigned spaces, the one labeled 'Transcription Factors Only' would be a transcription factor binding site.

How Do Transcription Factor Binding Sites Work?

Transcription factor binding sites are a part of either the promoter or enhancer region of a gene. A gene promoter sits upstream to a gene and contains three important regions. These are the regulatory protein binding site, the transcription factor binding site, and the RNA polymerase binding site. Figure 1 shows a stylized picture of a promoter and enhancer. An enhancer is usually far upstream of a gene. Binding of transcription factors to an enhancer will stimulate transcription at a higher rate than if only the promoter was bound. So, binding of a TF to an enhancer means 'go faster!'

Transcription Factor Binding Sites
Image of a Transcription Factor Binding Site

A single TF can't start transcription. In fact, many proteins are needed. Once the first TF is bound, secondary factors will bind in a predetermined order. This results in the formation of a transcription complex. Once this complex is created, RNA polymerase can bind to the DNA and start transcription. Transcription is the way DNA becomes a DNA product, either protein or RNA. It is like making a photo copy of a book page. Turning on or off transcription is the way we regulate gene expression.

How Do We Find Transcription Factor Binding Sites?

There are many ways to figure out if a particular piece of DNA is or has a transcription factor binding site within it. You can actually do a browser search for several different programs which will analyze a stretch of DNA sequence. These programs take the sequence you submit and predict whether or not there is a transcription factor binding site based on several different algorithms. Looking for transcription factor binding sites in this way is considered an in silico approach. In silico is an expression used to mean 'performed on computer or via computer simulation.'

Once you identify a transcription factor binding site, you need to prove that it is indeed a transcription factor binding site. Again, there are several methods for doing this. One of the easiest and best ways is to make a mutation in the transcription factor binding site which will make the transcription factor that binds to it unable to do so. This will test whether you have really identified a transcription factor binding site or not.

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