What is the Difference Between Upstream and Downstream DNA

The main difference between upstream and downstream DNA is that the upstream DNA is the DNA which occurs towards the 5’ end from a particular point on the DNA strand whereas the downstream DNA is the DNA which occurs towards the 3’ end. Furthermore, the upstream DNA from the transcription initiation site of a gene contains regulatory elements while the downstream DNA from this point contains the protein-coding region, which has been transcribed during transcription.

Upstream and downstream DNA are the two types of DNA classified based on the position of DNA with respect to a particular point.

Key Areas Covered

1. What is Upstream DNA
     – Definition, Relative Position, Features
2. What is Downstream DNA
     – Definition, Relative Position, Features
3. What are the Similarities Between Upstream and Downstream DNA
     – Outline of Common Features
4. What is the Difference Between Upstream and Downstream DNA
     – Comparison of Key Differences

Key Terms

Downstream DNA, 3’ End, 5’ End, Protein-Coding Region, Regulatory Elements, Transcription Initiation Site, Upstream DNA

What is Upstream DNA

Upstream DNA is the DNA which occurs towards the 5’ end from a particular point on the DNA strand. Significantly, the term upstream DNA is used to describe the DNA which occurs towards the 5’ end from the transcription initiation site. And, this DNA mainly contain the regulatory elements of a gene, including the promoter site and the transcription binding sites like enhancers. Therefore, the main function of this DNA is to regulate the gene expression at the transcriptional level.

Figure 1: Upstream and Downstream DNA

On the contrary, RNA molecules also have upstream RNA which occurs towards the 5’ position of the RNA molecule.

What is Downstream DNA

Downstream DNA is the DNA which occurs towards the 3’ end from a particular point on the DNA. Moreover, we consider the DNA which occurs towards the 3’ end from the transcription initiation site as the downstream DNA of a gene. The downstream DNA of a gene contains the protein-coding region of the gene. In eukaryotes, it contains exons and introns. The protein-coding region undergoes transcription to produce a functional RNA molecule, which can be either an mRNA, rRNA or tRNA. Also, the protein-coding region ends at the transcription termination site, which is another functional element on the downstream DNA. In a general sense, it is a type of regulatory element signaling the end of transcription.

Figure 2: Transcription Initiation Site

Also, downstream DNA occurs towards the 3’ end of the RNA molecules.

Similarities Between Upstream and Downstream DNA

• Upstream and downstream DNA are the two types of DNA classified based on the position of DNA with respect to a particular point.
• Both types of DNA are made up of a sequence of nucleotides.
• Also, they both encode for different functional elements.
• Furthermore, upstream DNA can be downstream DNA with the point considered and vice versa.
• Besides, we often use these terms in describing the DNA in either side of the transcription initiation site.

Difference Between Upstream and Downstream DNA

Definition

Upstream DNA refers to the DNA towards the 5’ end while downstream DNA refers to the DNA towards the 3’ end. Thus, this is the main difference between upstream and downstream DNA.

Elements With Respect to the Transcription Initiation Site

Upstream DNA contains regulatory elements including the promoter, and transcription factor-binding sites while downstream DNA contains the protein-coding region.

Transcription

Transcription is another difference between upstream and downstream DNA. Upstream DNA to the transcription initiation site does not undergo transcription while downstream DNA to the transcription initiation site undergoes transcription up to the transcription termination site.

Numbering

Positions of the nucleotides of the upstream DNA are stated with negative numbers starting from the transcription initiation site while positions of the nucleotides of the downstream DNA are stated with positive numbers starting from the transcription initiation site.

Function

The main function of the upstream DNA from the transcription initiation site is to regulate transcription while the corresponding downstream DNA contains information for the production of a functional molecule including proteins or RNA. Hence, this is another difference between upstream and downstream DNA.

Conclusion

Upstream DNA is the DNA which occurs towards the 5’ end with respect to a particular point. The upstream DNA to the transcription initiation site contains regulatory elements of the gene including the promoter and the transcription factor-binding sites. Here, downstream DNA is the DNA which occurs towards the 3’ end from the transcription initiation site. This DNA contains the protein-coding region. Therefore, the main difference between upstream and downstream DNA is the relative position of DNA with respect to a particular point on the DNA strand.

References:

1. “Upstream/Downstream.” GenScript, Available Here

Image Courtesy:

1. “Upstream and downstream” By Kelvinsong – Own work (CC0) via Commons Wikimedia  
2. “Figure 15 02 01” By CNX OpenStax – http://cnx.org/contents/[email protected]:rZudN6XP@2/Introduction (CC BY 4.0) via Commons Wikimedia