Transcription is the process cells use to make an RNA copy of genetic information stored in DNA. It is the first major step in gene expression, allowing the information in a gene to be used to produce RNA molecules and, for protein-coding genes, ultimately proteins.
The central enzyme in transcription is RNA polymerase. It moves along a DNA template strand, using the DNA sequence to assemble a complementary RNA strand. Transcription is commonly described in three stages: initiation, elongation, and termination.
Although the basic process is shared across organisms, the details differ between bacteria and eukaryotic cells. Eukaryotic transcription, for example, involves additional regulatory proteins and occurs in the nucleus, while bacterial transcription occurs in the cytoplasm because bacteria do not have a nucleus.
What happens during transcription?
DNA contains two complementary strands. During transcription, RNA polymerase uses one of them as the template strand. The RNA sequence is complementary to that template, although RNA contains the base uracil (U) instead of thymine (T).
The resulting RNA is therefore nearly identical in sequence to the DNA strand opposite the template, called the coding strand, except that U replaces T.
RNA polymerase does not need a separate primer to begin transcription. Instead, it recognizes specific DNA sequences that mark where transcription should begin and then starts building the RNA strand.
The process can be divided into three stages:
- Initiation: RNA polymerase is positioned at the gene and begins RNA synthesis.
- Elongation: RNA polymerase moves along the DNA template and extends the RNA molecule.
- Termination: RNA polymerase receives signals to stop transcription and releases the completed RNA.
Initiation: starting transcription
Initiation determines where transcription begins. The process starts when RNA polymerase is recruited to a particular region of DNA associated with the gene.
Promoters mark where transcription begins
A promoter is a DNA sequence near the beginning of a gene that helps direct the transcription machinery. It provides a recognition site for the proteins and molecular machinery responsible for initiating transcription.
In bacteria, RNA polymerase recognizes promoters with the help of a protein called a sigma factor. The sigma factor helps the polymerase identify the appropriate promoter and position itself correctly. Once transcription begins, the polymerase eventually moves away from the promoter and proceeds into the gene.
Eukaryotic cells use a more elaborate system. RNA polymerase II, the enzyme responsible for transcribing most protein-coding genes, generally requires several general transcription factors to assemble at the promoter and recruit or position the polymerase. Regulatory proteins can also influence whether and how efficiently a gene is transcribed.
The DNA opens locally
Once the transcription machinery is properly positioned, a small section of the DNA double helix is unwound. This creates access to the template strand.
RNA polymerase then begins linking RNA nucleotides together, matching them to the exposed DNA template. The first RNA nucleotides are joined through phosphodiester bonds, the same type of covalent linkage that forms the backbone of nucleic acids.
Initiation ends once the polymerase has successfully begun moving away from the promoter and entered the elongation phase.
Elongation: building the RNA strand
During elongation, RNA polymerase travels along the DNA template while continuously extending the RNA molecule.
The polymerase reads the template DNA in the 3′ to 5′ direction and synthesizes RNA in the 5′ to 3′ direction. This directionality is a fundamental feature of nucleic acid synthesis.
As the polymerase moves, it temporarily separates a small portion of the DNA strands. New RNA nucleotides enter the active site of the enzyme and pair with their complementary bases on the DNA template:
- DNA A pairs with RNA U
- DNA T pairs with RNA A
- DNA C pairs with RNA G
- DNA G pairs with RNA C
The newly formed RNA separates from the DNA template as the polymerase moves forward, while the DNA strands behind the enzyme re-form their double helix.
RNA polymerase does more than copy DNA
Transcription is not simply a process of copying an entire chromosome. RNA polymerase transcribes specific regions of DNA according to signals that determine where transcription begins and ends.
The sequence of the resulting RNA depends on the DNA template, but the amount and timing of transcription are heavily regulated. Cells can therefore control which genes are transcribed and how much RNA is produced from them.
In eukaryotic cells, the initial RNA produced from a protein-coding gene is usually called pre-mRNA. It undergoes additional processing before becoming mature messenger RNA (mRNA). Important processing events include addition of a 5′ cap, removal of introns through splicing, and formation of a 3′ poly(A) tail.
These processing steps are distinct from transcription itself, although they are closely coordinated with transcription in eukaryotic cells.
Termination: ending transcription
Transcription ends when RNA polymerase encounters signals that cause it to stop and release the RNA molecule.
The mechanism differs between bacteria and eukaryotes.
Termination in bacteria
Bacteria use several termination mechanisms. In one important mechanism, the newly produced RNA forms a structure that contributes to stopping the polymerase. Another mechanism involves a protein called Rho, which helps bring transcription to an end.
The precise mechanism depends on the bacterial gene and its regulatory sequences.
Termination in eukaryotes
For genes transcribed by RNA polymerase II, termination is closely associated with processing of the newly made RNA. The polymerase transcribes beyond the sequence that specifies the eventual 3′ end of the mRNA. The RNA is then cleaved, and subsequent events lead to termination and release of the polymerase from the DNA.
This is one reason transcription in eukaryotic cells is more accurately viewed as a coordinated process involving RNA synthesis, RNA processing, and changes in the transcription machinery rather than as three completely isolated steps.
How the three stages fit together
The three stages describe a continuous molecular process rather than three independent events.
Initiation establishes the starting point. Regulatory proteins and RNA polymerase identify the appropriate gene and promoter, and the DNA is locally opened.
Elongation produces the RNA. RNA polymerase travels along the template strand, adding RNA nucleotides to the growing transcript in the 5′ to 3′ direction.
Termination ends transcription. Signals associated with the gene cause the transcription machinery to stop, and the RNA transcript is released or processed as part of the termination process.
Together, these stages allow genetic information in DNA to be selectively converted into RNA. In protein-coding genes, that RNA can then serve as the template for translation, linking transcription to the production of proteins.
