Transcription of DNA & Central Dogma

The Central dogma explains how the DNA codes for the proteins which proceed in three stages,
namely, replication, transcription and translation. Once DNA replicates its two strands, the
information is copied into RNA by the process called transcription.

Transcription

Transcription is the first step of gene expression. During this process, the DNA sequence of a
gene is copied into RNA. Before transcription can take place, the DNA double helix must
unwind near the gene that is getting transcribed. The region of opened-up DNA is called
a transcription bubble.

In transcription, a region of DNA opens up. One strand, the template strand, serves as a template
for synthesis of a complementary RNA transcript. The other strand, the coding strand, is identical
to the RNA transcript in sequence, except that it has uracil (U) bases in place of thymine (T)
bases.

Example:
Coding strand: 5'-ATGATCTCGTAA-3' Template strand: 3'-TACTAGAGCATT-5' RNA
transcript: 5'-AUGAUCUCGUAA-3'

In translation, the RNA transcript is read to produce a polypeptide.

Example:

RNA transcript: 5'-AUG AUC UCG UAA-3' Polypeptide: (N-terminus) Met - Ile - Ser - [STOP]
(C-terminus)

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 (or coding) strand. However, there is
one important difference: in the newly made RNA, all of the T nucleotides are replaced with U
nucleotides.

The site on the DNA from which the first RNA nucleotide is transcribed is called the 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 said to be downstream.

If the gene that's transcribed encodes a protein (which many genes do), the RNA molecule will
be read to make a protein in a process called translation.

RNA polymerase
RNA polymerases are enzymes that transcribe DNA into RNA. Using a DNA template, RNA
polymerase builds a new RNA molecule through base pairing. For instance, if there is a G in the
DNA template, RNA polymerase will add a C to the new, growing RNA strand.
RNA polymerase synthesizes an RNA strand complementary to a template DNA strand. It
synthesizes the RNA strand in the 5' to 3' direction, while reading the template DNA strand in the
3' to 5' direction. The template DNA strand and RNA strand are antiparallel.

RNA transcript: 5'-UGGUAGU...-3' (dots indicate where nucleotides are still being added at 3'
end) DNA template: 3'-ACCATCAGTC-5'

RNA polymerase always builds a new RNA strand in the 5’ to 3’ direction. That is, it can only
add RNA nucleotides (A, U, C, or G) to the 3' end of the 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. Plants have an additional two
kinds of RNA polymerase, IV and V, which are involved in the synthesis of certain small RNAs.

Transcription initiation

To begin transcribing a gene, RNA polymerase binds to the DNA of the gene at a region called
the promoter. Basically, the promoter tells the polymerase where to "sit down" on the DNA and
begin transcribing.
The promoter region comes before (and slightly overlaps with) the transcribed region whose
transcription it specifies. It contains recognition sites for RNA polymerase or its helper proteins
to bind to. The DNA opens up in the promoter region so that RNA polymerase can begin
transcription.

Each gene (or, in bacteria, each group of genes transcribed together) has its own promoter. A
promoter contains DNA sequences that let RNA polymerase or its helper proteins attach to the
DNA. Once the transcription bubble has formed, the polymerase can start transcribing.

Promoters in bacteria

To get a better sense of how a promoter works, let's look an example from bacteria. A typical
bacterial promoter contains two important DNA sequences, the and elements.

RNA polymerase recognizes and binds directly to these sequences. The sequences position the
polymerase in the right spot to start transcribing a target gene, and they also make sure it's
pointing in the right direction.

Once the RNA polymerase has bound, it can open up the DNA and get to work. DNA opening
occurs at the element, where the strands are easy to separate due to the many As and Ts (which
bind to each other using just two hydrogen bonds, rather than the three hydrogen bonds of Gs
and Cs).
Bacterial promoter. The promoter lies at the start of the transcribed region, encompassing the
DNA before it and slightly overlapping with the transcriptional start site. The promoter contains
two elements, the -35 element and the -10 element. The -35 element is centered about 35
nucleotides upstream of (before) the transcriptional start site (+1), while the -10 element is
centered about 10 nucleotides before the transcriptional start site. In this particular example, the
sequence of the -35 element (on the coding strand) is 5'-TTGACG-3', while the sequence of the -
10 element (on the coding strand) is 5'-TATAAT-3'. The RNA polymerase has regions that
specifically bind to the -10 and -35 elements.

The minus signs just mean that they are before, not after, the initiation site.

Promoters in humans

In eukaryotes like humans, the main RNA polymerase in your cells does not attach directly to
promoters like bacterial RNA polymerase. Instead, helper proteins
called basal (general) transcription factors bind to the promoter first, helping the RNA
polymerase in your cells get a foothold on the DNA.

Many eukaryotic promoters have a sequence called a TATA box. The TATA box plays a role
much like that of the element in bacteria. It's recognized by one of the general transcription
factors, allowing other transcription factors and eventually RNA polymerase to bind. It also
contains lots of As and Ts, which make it easy to pull the strands of DNA apart.
The promoter of a eukaryotic gene is shown. The promoter lies upstream of and slightly overlaps
with the transcriptional start site (+1). It contains a TATA box, which has a sequence (on the
coding strand) of 5'-TATAAA-3'. The first eukaryotic general transcription factor binds to the
TATA box. Then, other general transcription factors bind. Finally, RNA polymerase II and some
additional transcription factors bind to the promoter.

Elongation

Once RNA polymerase is in position at the promoter, the next step of transcription—elongation
—can begin. Basically, elongation is the stage when the RNA strand gets longer, thanks to the
addition of new nucleotides.

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.
RNA polymerase synthesizes an RNA transcript complementary to the DNA template strand in
the 5' to 3' direction. It moves forward along the template strand in the 3' to 5' direction, opening
the DNA double helix as it goes. The synthesized RNA only remains bound to the template strand
for a short while, then exits the polymerase as a dangling string, allowing the DNA to close back
up and form a double helix.

In this example, the sequences of the coding strand, template strand, and RNA transcript are:

Coding strand: 5' - ATGATCTCGTAA-3'

Template strand: 3'-TACTAGAGCATT-5'

RNA: 5'-AUGAUC...-3' (the dots indicate where nucleotides are still being added to the RNA
strand at its 3' end)

The RNA transcript is nearly identical to the non-template, or coding, strand of DNA. However,
RNA strands have the base uracil (U) in place of thymine (T), as well as a slightly different sugar
in the nucleotide. So, as we can see in the diagram above, each T of the coding strand is replaced
with a U in the RNA transcript.
Transcription termination

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

Termination in bacteria

There are two major termination strategies found in bacteria: Rho-dependent and Rho-
independent.

In Rho-dependent termination, the RNA contains a binding site for a protein called Rho factor.
Rho factor binds to this sequence and starts "climbing" up the transcript towards RNA
polymerase.

Rho-dependent termination. The terminator is a region of DNA that includes the sequence that
codes for the Rho binding site in the mRNA, as well as the actual transcription stop point (which
is a sequence that causes the RNA polymerase to pause so that Rho can catch up to it). Rho binds
to the Rho binding site in the mRNA and climbs up the RNA transcript, in the 5' to 3' direction,
towards the transcription bubble where the polymerase is. When it catches up to the polymerase,
it will cause the transcript to be released, ending transcription.

When it catches up with the polymerase at the transcription bubble, Rho pulls the RNA transcript
and the template DNA strand apart, releasing the RNA molecule and ending transcription.
Another sequence found later in the DNA, called the transcription stop point, causes RNA
polymerase to pause and thus helps Rho catch up.

Rho-independent termination depends on specific sequences in the DNA template strand. As

Rho-independent termination. The terminator DNA sequence encodes a region of RNA that folds
back on itself to form a hairpin. The hairpin is followed by a series of U nucleotides in the RNA
(not pictured). The hairpin causes the polymerase to stall, and the weak base pairing between the
A nucleotides of the DNA template and the U nucleotides of the RNA transcript allows the
transcript to separate from the template, ending transcription.

In a terminator, the hairpin is followed by a stretch of U nucleotides in the RNA, which match up
with A nucleotides in the template DNA. The complementary U-A region of the RNA transcript
forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase,
produces enough instability for the enzyme to fall off and liberate the new RNA transcript.