Key Difference – Upstream vs Downstream DNA
It is important to have a general knowledge about the composition and structure of DNA in order to understand the difference between upstream and downstream DNA. DNA is composed of polynucleotide chains. Nucleotides are the building blocks which create polynucleotide chains and each nucleotide is made from three components: a five-carbon sugar, a nitrogenous base, and a phosphate group. A phosphate group and an OH group are attached to 5’ position carbon and 3’ position carbon of the sugar molecule in a nucleotide, respectively. Nucleotides are joined together by phosphodiester bonds formed between 5’ phosphate group of one nucleotide and 3’ OH group of the adjacent nucleotide. If a polynucleotide chain has a free 5’ phosphate group, it is assigned as the 5’ end; if it has a free 3’ OH group, it is assigned as a 3’ end. Therefore, DNA strands usually have 5’ and 3’ ends according to the end positions of the polynucleotide chains. DNA also exists as double-stranded form. Two strands are antiparallel to each other. Therefore, DNA has two strands which run towards 5’ to 3’ direction and 3’ to 5’ direction. Upstream and downstream DNA is referred with reference to transcription and synthesis of 5’ to 3’ mRNA strand. If DNA is considered towards the 5 end of the coding strand from the transcription initiation site it is known as upstream DNA. If DNA is considered towards the 3’ end from the coding strand from the transcription initiation site is known as downstream DNA. This is the key difference between upstream and downstream DNA.
CONTENTS
1. Overview and Key Difference
2. What is Upstream DNA
3. What is Downstream DNA
4. Side by Side Comparison – Upstream vs Downstream DNA
5. Summary
What is Upstream DNA?
A gene is a structural and functional unit heredity which is located on DNA of an organism. It is stored with instructions to construct a protein. The gene has a specific region of a DNA molecule. When required, it transcribes and translates into a protein via synthesis of an mRNA strand. Normally a coding strand of the gene runs from 5’ to 3’ direction. When it is transcribed, it produces an mRNA strand into the same direction 5’ to 3’. During the transcription, 3’ to 5’ antisense strand is served as the template strand and initiates the mRNA synthesis. There is a transcription initiation site in the gene. With reference to the transcription initiation site, the DNA region towards the 5’ end of the coding strand is known as upstream DNA. A promoter of the gene is normally located in the upstream region of DNA. In eukaryotic genes, there are TATA boxes, promoter proximal elements, and enhancers in the area upstream to the gene. The upstream region of the gene is referred with negative numbers. Upstream DNA of a gene is of utmost importance for the transcription.
What is Downstream DNA?
Transcription initiation site is known as +1 point of a gene. The DNA region from +1 point towards the 3’ end of the coding strand is known as downstream DNA. In other words, downstream of the gene is from the transcription initiation site towards the 5’ end of the template strand. Therefore, downstream DNA of a gene region includes transcriptional unit and other sequences such as terminator sequence. The promoter can influence the downstream sequence of a gene. Downstream part of a gene is referred with positive numbers. Downstream DNA of a gene is the actual region which gives the protein product.
Figure 01: Upstream and Downstream DNA
What is the difference between Upstream and Downstream DNA?
Upstream vs Downstream DNA |
|
| DNA region towards the 5’ end of the coding sequence from the transcription initiation site is known as upstream DNA. | DNA region towards the 3’ end of the coding strand from transcription initiation site is known as downstream DNA. |
| Elements | |
| Promoters and enhancers are located on the upstream DNA | Transcription unit and the terminator sequences are located in the downstream DNA. |
| Numbering | |
| Nucleotides in the upstream region are referred with negative numbers | Nucleotides are referred with positive numbers. |
| Function | |
| This region contains elements necessary to regulate and initiate transcription | This region contains instruction to produce a protein and terminate the transcription |
Summary – Upstream vs Downstream DNA
It is easy to identify upstream and downstream of an RNA strand. With regard to the reference site, the region towards the 5’ end of the RNA strand is known as upstream RNA whereas region towards the 3’ end is known as downstream RNA. However, in DNA, there are two strands that run in both directions 5’ to 3’ and 3’ to 5’. Hence, the difference between upstream and downstream DNA is complicated. Therefore, it is differentiated with reference to the transcription of a gene. From the transcription initiation site towards the 5 end of the sense strand, DNA region is known as upstream DNA whereas from the transcription initiation site towards the 3’ end of the sense strand is known as downstream DNA. This is the difference between upstream and downstream of DNA.
References:
1. Rhee, Amy C., Benjamin H. Somerlot, Neeta Parimi, and Jonatha M. Gott. “Distinct roles for sequences upstream of and downstream from Physarumediting sites.” RNA. Cold Spring Harbor Laboratory Press, Sept. 2009. Web. 18 Mar. 2017
Image Courtesy:
1. Barbosa, Cristina, Isabel Peixeiro, and Luísa Romão. “Gene Expression Regulation by Upstream Open Reading Frames and Human Disease.” PLOS Genetics. Public Library of Science, n.d. Web. 18 Mar. 2017.