What is the Difference Between Enhancer and Silencer

The main difference between enhancer and silencer is that an enhancer is a cis-regulatory sequence to which transcription factors bind to increase the activity of a gene, whereas a silencer is another cis-regulatory sequence to which transcription factors bind to decrease the activity of a gene. 

Enhancer and silencer are two transcription factors that bind to cis-regulatory sequences. They bind transcription factors to alter gene expression.    

Key Areas Covered

1. What is an Enhancer
– Definition, Structure, Function
2. What is a Silencer
– Definition, Structure, Function
3. Similarities Between Enhancer and Silencer
– Outline of Common Features
4. Difference Between Enhancer and Silencer
– Comparison of Key Differences

Key Terms 

Enhancer, Silencer

What is Enhancer

An enhancer is a cis-regulatory sequence element that increases the activity of a particular promoter. It is a short DNA sequence of about 50-1500 bp, and the transcription factors called activators can bind to it. The location of the enhancer can be up to 1 Mbp away from the promoter. It also can be upstream or downstream to the promoter. Although the location is far from the promoter, enhancers are spatially close to the promoter, allowing interactions with RNA polymerase and basal transcription factors. The activator proteins or transcription factors bound to the enhancer region then bind with a mediator complex, which recruits the RNA polymerase and the basal transcription factors to the promoter site. The orientation of the enhancer sequence does not influence this action.

Figure 1: Enhancer

Furthermore, the enhancer is a short region of DNA consisting of 50–1500 bp. The antagonists of the enhancers are the silencers. 

What is Silencer

A silencer is another cis-regulatory sequence that decreases the activity of a particular gene. Repressors are the type of transcription factors that bind to the silencers. The binding of repressors to the silencer region prevents the binding of RNA polymerase to the promoter. Therefore, it prevents the transcription. RNA polymerase is the enzyme that transcribes DNA sequences. Also, the silencer elements occur from -20 bp to -2000 bp upstream of the target gene. Certain silencers can occur downstream to the promoter within the introns and exons of the gene. Additionally, they can occur within the 3’ UTR.

Figure 2: Silencer

Moreover, there are two types of silencer elements. They are classic silencer elements and non-classical, negative regulatory elements. Classical silencers actively repress the gene. Also, they interfere with the assembly of general transcription factors. In contrast, a passive repression of genes occurs by the non-classical negative regulatory elements. 

Similarities Between Enhancer and Silencer

• Enhancer and silencer are two transcription factors that bind to the cis-regulatory sequences.
• They bind transcription factors.
• Also, they alter gene expression.

Difference Between Enhancer and Silencer

Definition

Enhancer refers to a DNA sequence that increases the transcription level of a gene located nearby on the same chromosome. In contrast, silencer refers to regulatory DNA elements that reduce transcription from their target promoters. 

Function

Binding transcription factors to an enhancer increases the transcription level, while binding transcription factors to a silencer decreases the transcription level.  

Structure 

The enhancer is 100 bp to 300 bp long (or longer) and consists of a string of binding sites for DNA-binding activator proteins or transcription factors. In comparison, silencer occurs -20 bp to -2000 bp upstream of a gene. 

Conclusion

In brief, enhancer and silencer are two cis-regulatory sequences that alter gene expression upon binding to transcription factors. Enhancer increases transcriptional level. It is 100 bp to 300 bp long. It contains a string of binding sites to the transcription factors. In comparison, a silencer decreases the transcription level. It occurs from -20 bp to -2000 bp upstream of a gene. Therefore, enhancer and silencer have their effect on transcription. 

References:

1. Friedman RZ, Granas DM, Myers CA, Corbo JC, Cohen BA, White MA. Information content differentiates enhancers from silencers in mouse photoreceptors. Elife. 2021 Sep 6;10:e67403. doi: 10.7554/eLife.67403. PMID: 34486522; PMCID: PMC8492058.

Image Courtesy:

1. “Regulation of transcription in mammals” By Bernstein0275 – Own Work (CC-BY SA 4.0) via Commons Wikimedia
2. “Biology-02-00064-g001” By Guest2625 – Own work (CC BY 3.0) via Commons Wikimedia