Transcription is the process of the formation of RNA from DNA. It has three main steps that are initiation, elongation, and termination. Prokaryotic transcription takes place in the nucleoid where their DNA molecule is present with the help of RNA polymerase.  Eukaryotic transcription is carried out in the nucleus of the cell by one of three RNA polymerases, depending on the RNA being transcribed.

Prokaryotic transcription

Initiation: A promoter is a DNA sequence onto which the transcription machinery binds and initiates transcription. 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, there are two promoter consensus sequences. The -10 consensus sequence, called the -10 region, is TATAAT. The -35 sequence, TTGACA, is recognized and bound by σ. Once this interaction is made, the subunits of the core enzyme bind to the site. The A–T-rich -10 region facilitates unwinding of the DNA template; several phosphodiester bonds are made. The transcription initiation phase ends with the production of abortive transcripts, which are polymers of approximately 10 nucleotides that are made and released.

Elongation: The transcription elongation phase begins with the release of the σ subunit from the polymerase. The dissociation of σ allows the core RNA polymerase enzyme to proceed along with the DNA template, synthesizing mRNA in the 5′ to 3′ direction at a rate of approximately 40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it. Since the base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components, RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely.

Termination: Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, 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 tracks along 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 and it stalls. 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–G nucleotides.

Eukaryotic transcription

Initiation: 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 help 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-extensively studied core 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, as a core promoter element, is the binding site for a transcription factor known as TATA-binding protein (TBP), which is itself a subunit of another transcription factor: Transcription Factor II D. After TFIID binds to the TATA box via the TBP, five more transcription factors and RNA polymerase combine around the TATA box in a series of stages to form a pre-initiation complex. One transcription factor, Transcription Factor II H (TFIIH), is involved in separating opposing strands of double-stranded DNA to provide the RNA Polymerase access to a single-stranded DNA template.

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 all of the rRNAs except for the 5S rRNA molecule.

RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. Eukaryotic pre-mRNAs undergo extensive processing after transcription, but before translation.

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. The tRNAs have a critical role in translation: they serve as the adaptor molecules between the mRNA template and the growing polypeptide chain. Small nuclear RNAs have a variety of functions, including “splicing” pre-mRNAs and regulating transcription factors.

Elongation: RNA Polymerase II is a complex of 12 protein subunits. Specific subunits within the protein allow RNA Polymerase II to act as its own helicase, sliding clamp, single-stranded DNA binding protein, as well as carry out other functions. Consequently, RNA Polymerase II does not need as many accessory proteins to catalyze the synthesis of new RNA strands during transcription elongation as DNA Polymerase does to catalyze the synthesis of new DNA strands during replication elongation.

All RNA Polymerases travel along the template DNA strand in the 3′ to 5′ direction and catalyze the synthesis of new RNA strands in the 5′ to 3′ direction, adding new nucleotides to the 3′ end of the growing RNA strand.

RNA Polymerases unwind the double-stranded DNA ahead of them and allow the unwound DNA behind them to rewind. As a result, RNA strand synthesis occurs in a transcription bubble of about 25 unwound DNA base pairs. Only about 8 nucleotides of newly-synthesized RNA remain base-paired to the template DNA. The rest of the RNA molecules falls off the template to allow the DNA behind it to rewind.

RNA Polymerases use the DNA strand below them as a template to direct which nucleotide to add to the 3′ end of the growing RNA strand at each point in the sequence. The RNA Polymerase travels along the template DNA one nucleotide at a time. Whichever RNA nucleotide is capable of base pairing to the template nucleotide below the RNA Polymerase is the next nucleotide to be added. Once the addition of a new nucleotide to the 3′ end of the growing strand has been catalyzed, the RNA Polymerase moves to the next DNA nucleotide on the template below it. This process continues until transcription termination occurs.

Termination: The ribosomal rRNA genes transcribed by RNA Polymerase I contain a specific sequence of base pairs that is recognized by a termination protein called TTF-1 (Transcription Termination Factor for RNA Polymerase I.) This protein binds the DNA at its recognition sequence and blocks further transcription, causing the RNA Polymerase I to disengage from the template DNA strand and to release its newly-synthesized RNA.

The RNAs formed are of three types that are mRNA, tRNA, and rRNA.

mRNA is a type of RNA that acts as a messenger of DNA to send information or message for the formation of proteins. The mRNA moves to the cytoplasm towards the ribosomes and synthesize proteins by the process known as translation. tRNA or transfer RNA helps in the transfer of amino acids to the ribosomes for the synthesis of proteins. They match the codons of the mRNA with the amino acids the codons synthesize. It contains anticodons that detect the codons of mRNA. It has a specific cloverleaf like structure. rRNA does not code for amino acids. They act as the building blocks of the ribosomes that are the factory of protein synthesis. This RNA help in reading the amino acid sequence and bind or link them to synthesize proteins.

In eukaryotic transcription, a pre-mRNA is formed which is processed and converted into a messenger RNA or mRNA. At 5″ end of the pre mRNA, a modified guanine nucleotide is added which is known as a cap. It protects the mRNA and also helps in the attachment of the ribosomes to the mRNA while translation. At 3′ end of the pre mRNA, 100 to 200 adenine nucleotides are added known as poly-A tail. This tail provides stability to the mRNA.

Other than this, RNA splicing is also an important part of mRNA processing. During this, unnecessary or junk sequences of pre mRNA known as introns are removed. This is done by spliceosome which is a protein and RNA complex. The remaining parts that are not removed are known as extrons and these are joined to each other by the spliceosome. These result in the formation of final mRNA.

The availability of introns allows variation in the sequences of mRNA and thus, variation in protein formation. Based on evolution, introns may be coded for some amino acid sequences to synthesize proteins earlier but they are considered nonfunctional now.

The small nuclear RNAs are special types of RNAs that form complex with proteins to form small nuclear ribonucleoproteins. Many small nuclear ribonucleoproteins together form a molecule or an enzyme known as a spliceosome. The spliceosome helps in the processing of pre mRNA after transcription. The unwanted parts of pre mRNA known as introns are removed and the remaining parts known as extrons are joined to each other by the spliceosome.

Key Points

• The transcription of mRNA begins at the initiation site.
• Two promoter consensus sequences are at the -10 and -35 regions upstream of the initiation site in prokaryotes. The σ subunit of RNA polymerase recognizes and binds the -35 region.
• The transcription elongation phase begins with the dissociation of the σ subunit, which allows the core RNA polymerase enzyme to proceed along the DNA template.
• Termination can be protein-based or RNA-based.
• Rho-dependent termination is caused by the rho protein colliding 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 by the polymerase stalling at a stable hairpin formed by a region of complementary C–G nucleotides at the end of the mRNA.
• Eukaryotic transcription is carried out in the nucleus of the cell and proceeds in three sequential stages: initiation, elongation, and termination.
• Eukaryotes require transcription factors to first bind to the promoter region and then help recruit the appropriate polymerase.
• RNA Polymerase II is the polymerase responsible for transcribing mRNA.
• RNA polymerase II (RNAPII) transcribes the major share of eukaryotic genes.
• During elongation, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome.
• 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.
• 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).
• RNA Polymerase II terminates transcription at random locations past the end of the gene being transcribed. The newly-synthesized RNA is cleaved at a sequence-specified location and released before transcription terminates.
• mRNA is formed from one strand of DNA by a process known as transcription.
• tRNA helps in transferring amino acids to the ribosomes.
• rRNA acts as the building block of the ribosomes and also helps to read the sequence of amino acids and link them to synthesize the proteins.
• pre mRNA is formed which is processed to mRNA. During the processing of eukaryotic pre mRNA, a modified guanine residue is added as a cap at 5′ end of pre mRNA. It protects mRNA and helps in its binding to ribosomes for translation.
• At 5′ end, a poly-A tail made of 100 to 200 adenine residues is attached that provides strength.
• Introns are intervening sequences within a pre-mRNA molecule that do not code for proteins and are removed during RNA processing by a spliceosome.
• Exons are expressing sequences within a pre-mRNA molecule that are spliced together once introns are removed to form mature mRNA molecules that are translated into proteins.
• Introns help to create variation in mRNA and thus protein synthesis.
• Non-coding proteins may get coded from introns.
• Introns may have been useful and coded for some useful proteins but after evolution, they were no longer needed so removed in mRNA processing.
• Ribozymes are enzymes formed of RNA instead of proteins.
• Small nuclear RNAs form complex with proteins to form small nuclear ribonucleoproteins.
• The ribonucleoproteins form the spliceosome that removes introns and joins extrons during the processing of pre mRNA.

Key Terms

• RNA: It is a type of nucleic acid that helps in the synthesis of proteins in the cells.
• Transcription: It is the process of synthesis of mRNA from DNA.
• Translation: It is the process of synthesis of protein from mRNA.
• promoter: the section of DNA that controls the initiation of RNA transcription
• elongation: the addition of nucleotides to the 3′-end of a growing RNA chain during transcription
• polymerase: any of various enzymes that catalyze the formation of polymers of DNA or RNA using an existing strand of DNA or RNA as a template
• Codon: Sequence of three nucleotides that decides which amino acid will be synthesized.
• Ribosome: protein/mRNA complexes found in all cells that are involved in the production of proteins by translating messenger RNA.
• intron: a portion of a split gene that is included in pre-RNA transcripts but is removed during RNA processing and rapidly degraded
• exon: a region of a transcribed gene present in the final functional RNA molecule
• spliceosome: a dynamic complex of RNA and protein subunits that removes introns from precursor mRNA