What begins the process of transcription?

DNA or deoxyribonucleic acid is the molecule that codes genetic information. However, DNA can't directly order a cell to make proteins. It has to be transcribed into RNA or ribonucleic acid. RNA, in turn, is translated by cellular machinery to make amino acids, which it joins together to form polypeptides and proteins

Transcription is the first stage of the expression of genes into proteins. In transcription, an mRNA (messenger RNA) intermediate is transcribed from one of the strands of the DNA molecule. The RNA is called messenger RNA because it carries the "message," or genetic information, from the DNA to the ribosomes, where the information is used to make proteins. RNA and DNA use complementary coding where base pairs match up, similar to how the strands of DNA bind to form a double helix.

One difference between DNA and RNA is that RNA uses uracil in place of the thymine used in DNA. RNA polymerase mediates the manufacture of an RNA strand that complements the DNA strand. RNA is synthesized in the 5' -> 3' direction (as seen from the growing RNA transcript). There are some proofreading mechanisms for transcription, but not as many as for DNA replication. Sometimes coding errors occur.

There are significant differences in the process of transcription in prokaryotes versus eukaryotes.

• In prokaryotes (bacteria), transcription occurs in the cytoplasm. Translation of the mRNA into proteins also occurs in the cytoplasm. In eukaryotes, transcription occurs in the cell's nucleus. mRNA then moves to the cytoplasm for translation.
• DNA in prokaryotes is much more accessible to RNA polymerase than DNA in eukaryotes. Eukaryotic DNA is wrapped around proteins called histones to form structures called nucleosomes. Eukaryotic DNA is packed to form chromatin. While RNA polymerase interacts directly with prokaryotic DNA, other proteins mediate the interaction between RNA polymerase and DNA in eukaryotes.
• mRNA produced as a result of transcription is not modified in prokaryotic cells. Eukaryotic cells modify mRNA by RNA splicing, 5' end capping, and addition of a polyA tail.

• The two main steps in gene expression are transcription and translation.
• Transcription is the name given to the process in which DNA is copied to make a complementary strand of RNA. RNA then undergoes translation to make proteins.
• The major steps of transcription are initiation, promoter clearance, elongation, and termination.

Transcription can be broken into five stages: pre-initiation, initiation, promoter clearance, elongation, and termination:

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The first step of transcription is called pre-initiation. RNA polymerase and cofactors (general transcription factors) bind to DNA and unwind it, creating an initiation bubble. It's similar in appearance to what you get when you unwind strands of multi-ply yarn. This space grants RNA polymerase access to a single strand of the DNA molecule. Approximately 14 base pairs are exposed at a time.

Forluvoft / Wikimedia Commons / Public Domain

The initiation of transcription in bacteria begins with the binding of RNA polymerase to the promoter in DNA. Transcription initiation is more complex in eukaryotes, where a group of proteins called transcription factors mediates the binding of RNA polymerase and the initiation of transcription.

Ben Mills / Wikimedia Commons / Public Domain

The next step of transcription is called promoter clearance or promoter escape. RNA polymerase must clear the promoter once the first bond has been synthesized. The promoter is a DNA sequence that signals which DNA strand is transcribed and the direction transcription proceeds. Approximately 23 nucleotides must be synthesized before RNA polymerase loses its tendency to slip away and prematurely release the RNA transcript.

Forluvoft / Wikimedia Commons / Public Domain

One strand of DNA serves as the template for RNA synthesis, but multiple rounds of transcription may occur so that many copies of a gene can be produced.

Forluvoft / Wikipedia Commons / Public Domain

Termination is the final step of transcription. Termination results in the release of the newly synthesized mRNA from the elongation complex. In eukaryotes, the termination of transcription involves cleavage of the transcript, followed by a process called polyadenylation. In polyadenylation, a series of adenine residues or poly(A) tail is added to the new 3' end of the messenger RNA strand.

• Watson JD, Baker TA, Bell SP, Gann AA, Levine M, Losick RM (2013). Molecular Biology of the Gene (7th ed.). Pearson.
• Roeder, Robert G. (1991). "The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly". Trends in Biochemical Sciences. 16: 402–408. doi:10.1016/0968-0004(91)90164-Q
• Yukihara; et al. (1985). "Eukaryotic transcription: a summary of research and experimental techniques". Journal of Molecular Biology. 14 (21): 56–79.

DNA transcription is the process by which the genetic information contained within DNA is re-written into messenger RNA (mRNA) by RNA polymerase. This mRNA then exits the nucleus, where it acts as the basis for the translation of DNA. By controlling the production of mRNA within the nucleus, the cell regulates the rate of gene expression.

In this article, we will look at the process of DNA transcription, including the post-transcriptional modification of mRNA and its importance.

RNA Vs DNA

RNA, like DNA, is a polymer of three subunits joined by phosphodiester bonds. However, as detailed in the table below, there are key differences in the monomer units for each compound.

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Stages of Transcription

The process of DNA transcription can be split into 3 main stages: initiation, elongation & termination. These steps are also involved in DNA replication.

Initiation

Transcription is catalysed by the enzyme RNA polymerase, which attaches to and moves along the DNA molecule until it recognises a promoter sequence. This area of DNA indicates the starting point of transcription, and there may be multiple promoter sequences within a DNA molecule. Transcription factors are proteins that control the rate of transcription; they too bind to the promoter sequences with RNA polymerase.

Once bound to the promoter sequence, RNA polymerase unwinds a portion of the DNA double helix, exposing the bases on each of the two DNA strands.

Elongation

One DNA strand (the template strand) is read in a 3' to 5' (three-prime to five-prime) direction, and so provides the template for the new mRNA molecule. The other DNA strand is referred to as the coding strand. This is because its base sequence is identical to the synthesised mRNA, except for the replacement of thiamine bases with uracil.

RNA polymerase uses incoming ribonucleotides to form the new mRNA strand. It does this by catalysing the formation of phosphodiester bonds between adjacent ribonucleotides, using complementary base pairing (A to U, T to A, C to G, and G to C). Bases can only be added to the 3' end, so the strand elongates in a 5’ to 3’ direction.

Termination

Elongation continues until the RNA polymerase encounters a stop sequence. At this point, transcription stops, and the RNA polymerase releases the DNA template.

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Pre-translational mRNA processing

The mRNA which has been transcribed up to this point is referred to as pre-mRNA. Processing must occur to convert this into mature mRNA. This includes:

5' Capping

Capping describes the addition of a methylated guanine cap to the 5' end of mRNA. Its presence is vital for the recognition of the molecule by ribosomes, and to protect the immature molecule from degradation by RNAases.

Polyadenylation

Polyadenylation describes the addition of a poly(A) tail to the 3' end of mRNA. The poly(A) tail consists of multiple molecules of adenosine monophosphate. This helps to stabilise RNA, which is necessary as RNA is much more unstable than DNA.

Splicing

Splicing allows the genetic sequence of a single pre-mRNA to code for many different proteins, conserving genetic material. This process is sequence-dependent and occurs within the transcript. It involves:

• Removal of introns (non-coding sequences) via spliceosome excision
• Joining together of exons (coding sequence) by ligation

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By the end of transcription, mature mRNA has been made. This acts as the messaging system to allow translation and protein synthesis to occur.

Within the mature mRNA, is the open reading frame (ORF). This region will be translated into protein. It is translated in blocks of three nucleotides, called codons. At the 5’ and 3’ ends, there are also untranslated regions (UTRs). These are not translated during protein synthesis.

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Clinical Relevance - Phenylketonuria (PKU)

PKU occurs due to a single base pair substitution (G to A) in the enzyme phenylalanine hydroxylase. This results in intron skipping, producing unstable mRNA. PKU is one of several genetic conditions tested for in babies via the newborn blood spot (heel prick) test.

Individuals with phenylketonuria accumulate phenylalanine in their tissues, plasma, and urine. Phenylketones are also found in their urine. This results in intellectual disability, developmental delay, microcephaly, seizures, and hypopigmentation.

Treatment includes consuming diets low in phenylalanine and avoiding high-protein foods such as meat, milk, and eggs.

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