Transcription

The process of copying genetic information from one strand of the DNA into RNA is termed as
transcription. Here also, the principle of complementarity governs the process of transcription,
except the adenosine now forms base pair with uracil instead of thymine. However, unlike in the
process of replication, which once set in, the total DNA of an organism gets duplicated, in
transcription only a segment of DNA and only one of the strands is copied into RNA. This
necessitates defining the boundaries that would demarcate the region and the strand of DNA that
would be transcribed.
Why both the strands are not copied during transcription has the simple answer. First, if both
strands act as a template, they would code for RNA molecule with different sequences (Remember
complementarity does not mean identical), and in turn, if they code for proteins, the sequence of
amino acids in the proteins would be different. Hence, one segment of the DNA would be coding
for two different proteins, and this would complicate the genetic information transfer machinery.
Second, the two RNA molecules if produced simultaneously would be complementary to each
other, hence would form a double stranded RNA. This would prevent RNA from being translated
into protein and the exercise of transcription would become a futile one.

Transcription Unit
A transcription unit in DNA is defined primarily by the three regions in the DNA:
1. A Promoter
2. The Structural gene
3. A Terminator
There is a convention in defining the two strands of the DNA in the structural gene of a
transcription unit. Since the two strands have opposite polarity and the DNA-dependent RNA
polymerase also catalyse the polymerisation in only one direction, that is, 5'-3' , the strand that has
the polarity 3'-5' acts as a template, and is also referred to as template strand. The other strand
which has the polarity (5'-3') and the sequence same as RNA (except thymine at the place of uracil),
is displaced during transcription. Strangely, this strand (which does not code for anything) is
referred to as coding strand.
The promoter and terminator flank the structural gene in a transcription unit. The promoter is said
to be located towards 5'-end (upstream) of the structural gene. It is a DNA sequence that provides
binding site for RNA polymerase, and it is the presence of a promoter in a transcription unit that
also defines the template and coding strands. The terminator is located towards 3'-end
(downstream) of the coding strand and it usually defines the end of the process of transcription.

Fig: Schematic structure of transcription unit.

Prokaryotic transcription
There is single DNA-dependent RNA polymerase that catalyses transcription of all types of RNA
in bacteria. RNA polymerase binds to promoter and initiates transcription (Initiation). It uses

nucleoside triphosphates as substrate and polymerises in a template depended fashion following

the rule of complementarity. It somehow also facilitates opening of the helix and continues
elongation. Only a short stretch of RNA remains bound to the enzyme. Once the polymerases
reaches the terminator region, the nascent RNA falls off, so also the RNA polymerase. This results
in termination of transcription.
How is the RNA polymerases able to catalyse all the three steps, which are initiation, elongation
and termination? The RNA polymerase is only capable of catalysing the process of elongation. It
associates transiently with initiation-factor (sigma) and termination-factor (rho) to initiate and
terminate the transcription, respectively. Association with these factors alter the specificity of the
RNA polymerase to either initiate or terminate.

Initiation
Transcription requires the DNA double helix to partially unwind in the region of mRNA synthesis.
The region of unwinding is called a transcription bubble. The DNA sequence onto which the
proteins and enzymes involved in transcription bind to initiate the process is called a promoter.
Elongation

Transcription always proceeds from template strand. During elongation, an enzyme called RNA
polymerase proceeds along the DNA template adding nucleotides by base pairing with the DNA
template in a manner similar to DNA replication, with the difference that an RNA strand is being
synthesized that does not remain bound to the DNA template. As elongation proceeds, the DNA
is continuously unwound ahead of the core enzyme and rewound behind it.
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, but both involve repeated nucleotide sequences in the
DNA template that result in RNA polymerase leaving the DNA template, and freeing the mRNA
transcript. The termination of transcription occurs nonrandomly and takesplace at specific points
after the end of the coding sequence. In bacteria termination occurs at sequences known as
palindromes.
Both prokaryotes and eukaryotes perform fundamentally the same process of transcription, with
the important difference of the membrane-bound nucleus in eukaryotes. With the genes bound in
the nucleus, transcription occurs in the nucleus of the cell and the mRNA transcript must be
transported to the cytoplasm. The prokaryotes, which include bacteria and archaea, lack
membrane-bound nuclei and other organelles, and transcription occurs in the cytoplasm of the cell.
In both prokaryotes and eukaryotes, transcription occurs in three main stages: initiation,
elongation, and termination.
Eukaryotic transcription
In eukaryotes, there are two additional complexities (i) There are at least three RNA polymerases
in the nucleus (in addition to the RNA polymerase found in the organelles).
Eukaryotic transcription is carried out in the nucleus of the cell by one of three RNA polymerases,
depending on the RNA being transcribed, and proceeds in three sequential stages: Initiation,
Elongation, and Termination.
Initiation of Transcription in Eukaryotes

Unlike the prokaryotic 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
select appropriate polymerase. The completed assembly of transcription factors and RNA
polymerase bind to the promoter, forming a transcription initiation complex.
The most common type of core promoter 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, is the binding site for a transcription factor. One transcription factor, DNA helicase, is
involved in separating opposing strands of double-stranded DNA to provide access to a singlestranded DNA template. However, only a low rate of transcription is driven by the pre-initiation
complex alone. Other proteins known as activators and repressors are responsible for modulating
transcription rate. Activator proteins increase the transcription rate, and repressor proteins decrease
the transcription rate.

Elongation
Following the formation of the pre-initiation complex, the polymerase is released from the other
transcription factors, and elongation is allowed to proceed with the polymerase synthesizing premRNA in the 5' to 3' direction.
Although the enzymatic process of elongation is essentially the same in eukaryotes and
prokaryotes, the eukaryotic DNA template is more complex. When eukaryotic cells are not
dividing, their genes exist as a diffuse mass of DNA and proteins called chromatin. The DNA is
tightly packaged around charged histone proteins at repeated intervals. These DNAhistone
complexes, collectively called nucleosomes, are regularly spaced and include 146 nucleotides of
DNA wound around eight histones like thread around a spool. One way of coping with the
nucleosome is to disassemble it into separate histones and uncoil the gene before transcribing.
Termination
The termination of transcription is different for the different polymerases. Unlike in prokaryotes,
elongation by RNA polymerase (RNAP) in eukaryotes continues 1,0002,000 nucleotides beyond
the end of the gene being transcribed. Termination generally occurs once RNAP encounters a
polyadenylation signal (As) which occurs soon after the end of the gene.
Viral gene transcription
Transcription of the viral genes from the integrated provirus depends on host cell RNA polymerase
II which binds to sequences in the 5 LTR.

The reverse transcriptase of some retroviruses has a high error rate. This means many of the
genome copies produced are incapable of replicating themselves. This can be overcome by
complementation between the two genome copies present in each viral particle which can also
recombine with each other during reverse transcription. These features combined with a high
turnover rate enable HIV-1 to adapt to new environments such as selective pressure from
antibodies and drug treatments.