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Is the promoter region of a gene transcribed?


If the RNA polymerase attaches to the promoter region of the gene, would it form the initial mRNA portion soon after attachment by reading the promoter region? Or should it slide across the DNA then form the initial mRNA portion?

Also, does the RNA polymerase read DNA base pairs one by one and add the RNA base pairs to the chain one by one? Or, does it read groups of base pairs just like tRNA which reads triplet of bases during translation?

Similarly, is the terminator region transcribed too and then the process of transcription ends, or does the process end immediately after the RNA polymerase reaches the terminator region? How does the process end just by reading the terminator region?

So, should the promoter and terminator region of a gene be considered parts of the gene or separate entities?


would it form the initial mRNA portion soon after attachment by reading the promoter region?

The RNA Polymerase binds to the promoter, however since it is so large the front end of it hangs off the end of the promoter. When Transcription begins the promoter is not included, as the transcription process occurs at the front of the polymerase.

Also, does the RNA polymerase read DNA base pairs one by one and add the RNA base pairs to the chain one by one?

The RNA polymerase adds nucleoside triphosphate (NTP) one by one. As the picture shows below, there is only room for one NTP in the active site and once the correct NTP is placed it is added to the RNA chain.

How does the process end just by reading the terminator region?

The question of termination is dependent on the cell. Prokaryotes terminate in either a Rho independent or dependent process. Independently, a hairpin occurs in the RNA that breaks off the transcript, dependently, a Rho factor binds that causes termination. Eukaryotes are less well known, but it is generally believed that after the poly-A site there are also factors that bind and induce termination.

So, should the promoter and terminator region of a gene be considered parts of the gene or separate entities?

This question is slightly more about definitions that biology. The Oxford Engligh dictionary defines a gene as "The basic unit of heredity in living organisms". Since the promoter, non-coding, and non-translating regions are still paramount in getting the protein made, I would argue that they are still part of the gene and the larger hereditary unit.


Is the promoter region of a gene transcribed? - Biology

DNA is copied into RNA in a process called genetic transcription. To transcribe means to “put down something in writing.” The information in DNA is transcribed—or rewritten—into a smaller version (RNA) that can be used by the cell.

Learning Objectives

  • Understand the basic steps in the transcription of DNA into RNA
  • Describe the role of RNA polymerase
  • Understand the difference between pre-RNA and mRNA
  • Describe RNA post-translational modification and its purpose

Transcription takes place in the nucleus. It uses DNA as a template to make an RNA (mRNA) molecule. During transcription, a strand of mRNA is made that is complementary to a strand of DNA. Figure 1 shows how this occurs.

Figure 1. Overview of Transcription. Transcription uses the sequence of bases in a strand of DNA to make a complementary strand of mRNA. Triplets are groups of three successive nucleotide bases in DNA. Codons are complementary groups of bases in mRNA.


Just as the trp operon is negatively regulated by tryptophan molecules, there are proteins that bind to the promoter sequences that act as positive regulators to turn genes on and activate them. For example, when glucose is scarce, E. coli bacteria can turn to other sugar sources for fuel. To do this, new genes to process these alternate sugars must be transcribed. When glucose levels drop, cyclic AMP (cAMP) begins to accumulate in the cell. The cAMP molecule is a signaling molecule that is involved in glucose and energy metabolism in E. coli. Accumulating cAMP binds to the positive regulator catabolite activator protein (CAP) , a protein that binds to the promoters of operons which control the processing of alternative sugars. When cAMP binds to CAP, the complex then binds to the promoter region of the genes that are needed to use the alternate sugar sources (Figure). In these operons, a CAP-binding site is located upstream of the RNA-polymerase-binding site in the promoter. CAP binding stabilizes the binding of RNA polymerase to the promoter region and increases transcription of the associated protein-coding genes.

Transcriptional activation by the CAP protein. When glucose levels fall, E. coli may use other sugars for fuel but must transcribe new genes to do so. As glucose supplies become limited, cAMP levels increase. This cAMP binds to the CAP protein, a positive regulator that binds to a promoter region upstream of the genes required to use other sugar sources.


Promoter Structures for RNA Polymerases I and III

In eukaryotes, the conserved promoter elements differ for genes transcribed by RNA polymerases I, II, and III. RNA polymerase I transcribes genes that have two GC-rich promoter sequences in the -45 to +20 region. These sequences alone are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from -180 to -105 upstream of the initiation site will further enhance initiation. Genes that are transcribed by RNA polymerase III have upstream promoters or promoters that occur within the genes themselves.


Is the promoter region of a gene transcribed? - Biology

Transcription is the first step in gene expression, and is the process by which a gene’s DNA sequence is copied (transcribed) to make an RNA molecule.

Prokaryotic transcription and eukaryotic transcription differ in a number of ways, which will be discussed below. Both in pro and eukaryotic cells the process takes place in different places. In eukaryotic cells it takes place in the nucleus and in prokaryotic cells it takes place in the cytoplasm. Both types of transcription involve initiation, elongation, and termination. Before transcription can take place, the DNA double helix must unwind near the gene that is being transcribed. The region of opened-up DNA is called a transcription bubble. Transcription uses one of the two exposed DNA strands as a template this strand is called the template strand. The RNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand. However, there is one important difference: in the newly made RNA, all of the T (thymine) nucleotides are replaced with U (uracil) nucleotides.

The site on the DNA from which the first RNA nucleotide is transcribed is called the +1 site, or the initiation site. Nucleotides that come before the initiation site are given negative numbers and said to be upstream. Nucleotides that come after the initiation site are marked with positive numbers and are referred to as downstream.

Transcription is performed by enzymes called RNA polymerases. Using a DNA template, RNA polymerase builds a new RNA molecule through base pairing. For instance, if there is a G nucleotide in the DNA template, RNA polymerase will add a C nucleotide to the growing RNA strand. RNA polymerases are large enzymes with multiple subunits, even in simple organisms like bacteria. Humans and other eukaryotes have three different kinds of RNA polymerase: I, II, and III. Each one specializes in transcribing certain classes of genes. Take a look at a diagram of an RNA polymerase in action below:

To begin transcribing a gene, RNA polymerase binds to the DNA of the gene at a region called the promoter, which points out on the DNA where the polymerase should begin transcribing. Each gene (or, in bacteria, each group of genes transcribed together) has its own promoter. You can get a sense of where the promoter is located relative to the gene downstream of it in the image below:

Prokaryotic transcription initiation begins when the transcription machinery binds to the promoter region of a DNA sequence. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all the time, some of the time, or infrequently. Although promoters vary among prokaryotic genomes, a few elements are conserved. At the -10 and -35 regions upstream of the initiation site (that is, 10 and 35 nucleotides upstream of the site), there are two promoter consensus sequences.

Unlike the prokaryotic RNA polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then recruit the appropriate polymerase. The completed assembly of transcription factors and RNA polymerase bind to the promoter, forming a transcription pre-initiation complex (PIC).

The most well-studied promoter element in eukaryotes is a short DNA sequence known as a TATA box, found 25-30 base pairs upstream from the start site of transcription. The TATA box is the binding site for a transcription factor called TATA-binding protein (TBP). Several additional transcription factors and RNA polymerase combine around the TATA box to form the pre-initiation complex.

As mentioned earlier, there are three RNA polymerases in eukaryotes. RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes. RNA polymerase I synthesizes rRNAs. RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. RNA polymerase III is also located in the nucleus. This polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre-RNAs.

Once RNA polymerase is in position at the promoter, the next step of transcription—elongation—can begin.

During elongation, RNA polymerase “walks” along one strand of DNA, known as the template strand, in the 3′ to 5′ direction. For each nucleotide in the template, RNA polymerase adds a matching (complementary) RNA nucleotide to the 3′ end of the RNA strand, as shown below.

RNA polymerase will keep transcribing until it receives a stop signal. The process of ending transcription is called termination, and it happens once the polymerase transcribes a sequence of DNA known as a terminator.

In prokaryotes, there are two kinds of termination signals: one is protein-based and the other is RNA-based. Rho-dependent termination is controlled by the rho protein, which follows behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template, causing it to stall (or stop). As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble.

Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C and G nucleotides. The RNA transcribed from this region folds back on itself, and the complementary C and G form a stable hairpin that causes the polymerase to stall and fall off.

Termination in eukaryotes begins when a polyadenylation signal appears in the RNA transcript. This is a sequence of nucleotides that marks where an RNA transcript should end. The polyadenylation signal is recognized by an enzyme that cuts the RNA transcript nearby, releasing it from RNA polymerase before transcription actually terminates.

After termination, transcription is finished. An RNA transcript that is ready to be used in translation is called a messenger RNA (mRNA). In eukaryotes, newly transcribed RNAs must first undergo a series of processing steps to form the mature mRNA.

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• Transcription initiation occurs when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins).

• Transcription elongation occurs in a bubble of unwound DNA, where the RNA Polymerase uses one strand of DNA as a template to catalyze the synthesis of a new RNA strand in the 5′ to 3′ direction.

• Transcription ends in a process called termination, which depends on sequences in the RNA called terminators.

• In prokaryotes, two promoter consensus sequences are at the -10 and -35 regions upstream of the initiation site.

• Eukaryotic transcription is carried out in the nucleus of the cell.

• Eukaryotes require transcription factors to first bind to the promoter region and then help recruit the appropriate RNA polymerase.

• Termination in prokaryotes can be protein-based or RNA-based. Rho-dependent termination occurs when the rho protein collides with the stalled polymerase at a stretch of G nucleotides on the DNA template near the end of the gene. Rho-independent termination is caused the polymerase stalling at a stable hairpin formed by a region of complementary C and G nucleotides at the end of the mRNA.

• In eukaryotes, RNA Polymerase II is the polymerase responsible for transcribing mRNA that encodes proteins.

• In eukaryotes, RNA Polymerase I and RNA Polymerase III terminate transcription in response to specific termination sequences in either the DNA being transcribed (RNA Polymerase I) or in the newly-synthesized RNA (RNA Polymerase III).

Transcription: The first step in gene expression, where DNA is transcribed into RNA.

Prokaryotic: A single-celled organism that lacks membrane-bound organelles.

Eukaryotic : Organisms with membrane-bound organelles.

Initiation: The first stage of transcription when RNA polymerase binds to a DNA sequence.

Elongation: The addition of nucleotides to the 3′-end of a growing RNA chain during transcription.

Termination: The last stage of transcription when the production of an RNA transcript ends.

Transcription bubble: A region where the DNA helix has unwound near a gene that is being transcribed.

Template strand: The strand of exposed DNA that is used as a template during transcription.

Nontemplate strand: The complementary strand of exposed DNA that is not used as the template during transcription.

Initiation site: The site in a DNA sequence where the first RNA nucleotide is transcribed.

Upstream: Nucleotides that are located before the initiation site.

Downstream: Nucleotides that are located after the initiation site.

RNA polymerase: Any of various enzymes that catalyze the formation of polymers of RNA using an existing strand of DNA as a template.

-10 and -35 regions: In prokaryotes, the two promoter consensus sequences where RNA polymerase binds during initiation.

Transcription factors: Proteins that bind to the promoter region of DNA and help recruit RNA polymerase in eukaryotes.

Transcription pre-initiation complex (PIC): In eukaryotes, the completed assembly of transcription factors and RNA polymerase that bind to the promoter to initate transcription.

TATA box: The most well-understood promoter element in eukaryotes where the transcription pre-initiation complex forms.

TATA-binding protein (TBP) : A transcription factor that recognizes and binds to the TATA box during initiation.

Termination: The process by which transcription ends.

Terminator: A DNA sequence that marks the end of transcription.

Rho-dependent termination: In prokaryotes, protein-dependent transcription termination.

Rho-independent termination: In prokaryotes, protein-independent transcription termination that instead depends on the DNA sequence being transcribed.

Polyadenylation signal: In eukaryotes, a sequence of nucleotides in RNA that marks where the RNA transcript should end.

Messenger RNA (mRNA): An RNA transcript that is ready to be used for protein synthesis, or translation.


In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and a σ protein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin.

Which subunit of the E. coli polymerase confers specificity to transcription?


The RNA polymerase(s)

RNA is transcribed from DNA using an RNA polymerase (RNAP). In bacteria this is done by a single enzyme however, eukaryotes have muliple polymerases which are each responsible for a specific subset of RNAs. To gain this specificity, the eukaryotic RNAP can recognize and bind to specific promoter elements. This means that the promoter present in your plasmid backbone must to be compatible with the type of RNA that needs to be made: if you want mRNA (for gene expression) you need to use an RNAP II promoter, whereas small RNAs (such as shRNA) are transcribed from the RNAP III promoters. This post features promoters for general RNAP II and RNAP III transcription however, using viral LTRs as RNAP II promoters is commonly employed in lentiviral and retroviral constructs and we will discuss these in a future post on viral vector parts.


  • Core promoter - the minimal portion of the promoter required to properly initiate transcription
    • Transcription Start Site (TSS)
    • Approximately -34
    • A binding site for RNA polymerase
      • RNA polymerase I: transcribes genes encoding ribosomal RNA
      • RNA polymerase II: transcribes genes encoding messenger RNA and certain small nuclear RNAs
      • RNA polymerase III: transcribes genes encoding tRNAs and other small RNAs
      • Approximately -250
      • Specific transcription factor binding sites
      • Anything further upstream (but not an enhancer or other regulatory region whose influence is positional/orientation independent)
      • Specific transcription factor binding sites

      Prokaryotic promoters

      In prokaryotes, the promoter consists of two short sequences at -10 and -35 positions upstream from the transcription start site. Sigma factors not only help in enhancing RNAP binding to the promoter but helps RNAP target which genes to transcribe.

      • The sequence at -10 is called the Pribnow box, or the -10 element, and usually consists of the six nucleotides TATAAT. The Pribnow box is absolutely essential to start transcription in prokaryotes.
      • The other sequence at -35 (the -35 element) usually consists of the six nucleotides TTGACA. Its presence allows a very high transcription rate.
      • Both of the above consensus sequences, while conserved on average, are not found intact in most promoters. On average only 3 of the 6 base pairs in each consensus sequence is found in any given promoter. No promoter has been identified to date that has intact consensus sequences at both the -10 and -35 it is thought that this would lead to such tight binding by the sigma factor that the polymerase would be unable to initiate productive transcription.
      • Some promoters contain so-called "extended -10 element" (consensus sequence 5’-TGNTATAAT-3') the presence of the -35 element appears to be unimportant for transcription from the "extended -10" promoters.

      It should be noted that the above promoter sequences are only recognized by the sigma-70 protein that interacts with the prokaryotic RNA polymerase. Complexes of prokaryotic RNA polymerase with other sigma factors recognize totally different core promoter sequences.

      Probability of occurrence of each nucleotide

      Eukaryotic promoters

      Eukaryotic promoters are extremely diverse and are difficult to characterize. They typically lie upstream of the gene and can have regulatory elements several kilobases away from the transcriptional start site. In eukaryotes, the transcriptional complex can cause the DNA to bend back on itself, which allows for placement of regulatory sequences far from the actual site of transcription. Many eukaryotic promoters, but by no means all, contain a TATA box (sequence TATAAA), which in turn binds a TATA binding protein which assists in the formation of the RNA polymerase transcriptional complex. [1] The TATA box typically lies very close to the transcriptional start site (often within 50 bases).

      Eukaryotic promoter regulatory sequences typically bind proteins called transcription factors which are involved in the formation of the transcriptional complex. An example is the E-box (sequence CACGTG), which binds transcription factors in the basic-helix-loop-helix (bHLH) family (e.g. BMAL1-Clock, cMyc). [2]


      Is the promoter region of a gene transcribed? - Biology

      A promoter is a regulatory region of DNA located upstream (towards the 5' region) of of a gene, providing a control point for regulated gene transcription.

      The promoter contains specific DNA sequences that are recognized by proteins known as transcription factors. These factors bind to the promoter sequences, recruiting RNA polymerase, the enzyme that synthesizes the RNA from the coding region of the gene.

      1. Core promoter - the minimal portion of the promoter required to properly initiate transcription

      • Transcription Start Site (TSS)
      • Approximately -34
      • A binding site for RNA polymerase
      • General transcription factor binding sites

      2. Proximal promoter - the proximal sequence upstream of the gene that tends to contain primary regulatory elements

      Difference between Eukaryotic and Prokaryotic Promoters

      Prokaryotic promoters

      In prokaryotes, the promoter consists of two short sequences at -10 and -35 positions upstream from the transcription start site.

      • The sequence at -10 is called the Pribnow box, or the -10 element, and usually consists of the six nucleotides TATAAT. The Pribnow box is absolutely essential to start transcription in prokaryotes.
      • The other sequence at - 35 (the -35 element) usually consists of the six nucleotides TTGACA. Its presence allows a very high transcription rate.

      Eukaryotic promoters

      Eukaryotic promoters are extremely diverse and are difficult to characterize. They typically lie upstream of the gene and can have regulatory elements several kilobases away from the transcriptional start site. In eukaryotes, the transcriptional complex can cause the DNA to bend back on itself, which allows for placement of regulatory sequences far from the actual site of transcription. Many eukaryotic promoters, contain a TATA box (sequence TATAAA ), which in turn binds a TATA binding protein which assists in the formation of the RNA polymerase transcriptional complex. The TATA box typically lies very close to the transcriptional start site (often within 50 bases).


      Watch the video: Promoter and Termination Sites of Transcription (January 2022).