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Overview of transcription

Stages of transcription

Eukaryotic pre-mRNA
processing

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Translation

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Eukaryotic pre-mRNA processing

Introduction
Imagine that you run a book-making factory. Would a book be ready to leave the factory as soon as its
pages were printed? Probably not. At the least, you'd need to put on a front and back cover. Perhaps
you'd also need to remove some blank or messed-up pages generated during printing of the "good"
pages. Only after these steps were finished would the book be complete and ready to leave the
factory.
In eukaryotes, protein-coding RNA transcripts (RNA "copies" of the DNA sequence of a gene) must go
through a similar set of processing steps to become mature messenger RNAs (mRNAs) that can leave
the nucleus. First, "cap" and "tail" molecules are attached to the two ends of the transcript. These
molecules play a protective role similar to that of a book's front and back covers. Similarly, many
eukaryotic RNAs contain sequences called introns, which must be removed from the transcript before
translation. Introns are somewhat like blank or throwaway pages generated during printing, which
must be removed to assemble the finished book.
In this article, we'll take a closer look at the cap, tail, and splicing modifications that eukaryotic RNA
transcripts undergo, seeing how these modifications are carried out and why they are important for
correct gene expression.

Overview of pre-mRNA processing in eukaryotes

An RNA transcript that is ready to be used in translation is called a messenger RNA (mRNA). In
bacteria, RNA transcripts are ready to act as messenger RNAs and undergo translation right away. In
eukaryotes, however, the transcripts produced by RNA polymerase II are called pre-mRNAs. As the
name suggests, pre-mRNAs do not yet count as mRNAs and must undergo additional processing
steps before they can be translated into proteins.

In the nucleus, pre-mRNAs are converted to mRNAs by a set of specialized enzymes. Some of these
enzymes modify the ends of the transcript, while others splice it (remove certain chunks of DNA and
paste the remaining chunks back together). Once the pre-mRNA has undergone all of these
processing steps, it is considered an mRNA and can be exported from the nucleus to the cytosol for
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translation.
Yes

5' cap and poly-A tail

No

Both ends of a pre-mRNA are modified by the addition of chemical groups. The group on the 5' end is
called a cap, while the group on the 3' end is called a tail. Both the cap and the tail protect the
transcript and ensure that it will be exported from the nucleus and translated inside the ribosomes.
First, shortly after transcription starts, an enzyme attaches a 5 cap to the first nucleotide in the
transcript. This cap, which is a modified version of a guanine nucleotide, makes the transcript more
stable by protecting it from degradation (breakdown). The 5' cap will also help the ribosome bind to
the mRNA at the start of translation.

The 3 end of the pre-mRNA is also modified. As described in the section on transcription termination,
the 3' end of the mRNA is formed when a sequence called a polyadenylation signal (AAUAAA)
appears in the mRNA. This sequence is recognized by an enzyme that cuts the RNA strand, releasing
it from RNA polymerase II. Another enzyme then adds 100 - 200 adenine (A) nucleotides to the 3
end, or cut end, of the transcript. This modification is called a poly-A tail, and it stabilizes the transcript
and promotes its export to the cytosol.

RNA splicing
The third major RNA processing event in eukaryotes is known as RNA splicing. In RNA splicing,
certain regions of the pre-mRNA transcript, known as introns, are cut out and removed by a
specialized enzyme complex known as the spliceosome (more below). The regions of the transcript
that are not removed, known as exons, are stitched back together by the spliceosome to form the
intact, protein-coding transcript. [Does DNA also have introns and exons?]

Thus, only the exons of a gene encode a polypeptide. The introns do not contribute to the sequence
of the polypeptide. In fact, they must be removed in order to produce a mature mRNA with the correct
sequence. An easy way to remember the difference between introns and exons is that introns are
intervening or interrupting sequences, while exons are what exit the nucleus as part of the mature
mRNA.
[What happens if the introns are not removed?]

To ensure that each mRNA has the right nucleotide sequence (and thus specifies the right series of
amino acids during translation), splicing must be precise and consistent. This careful cutting and
pasting is performed by the spliceosome, an enzyme complex made of protein and small RNAs. Most
introns contain marker sequences at both of their ends, which are recognized by the small RNAs and
direct the spliceosome to remove the intron. Once the intron has been cut out, the spliceosome will
"glue" (ligate) the flanking exons together.
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Yes

Alternative splicing

No

Many of the genes in a eukaryotic genome can undergo alternative splicing, meaning that different
portions of the pre-mRNA can be treated as exons and retained in the processed transcript. This
process leads to the production of different mRNAs, each of which encodes a different version of a
polypeptide.
In the figure below, the pre-mRNA at the top has five segments that may be treated as exons. These
segments can be retained or removed in different combinations, leading to the three different mRNAs
shown in the middle row, which encode the three distinct proteins at the bottom.

Image credit: "DNA, alternative splicing," by the National Human Genome Research Institute (public
domain).
In some cases, a single cell may produce all of the alternatively spliced mRNAs (and associated
proteins) encoded by a particular gene. In other cases, different cell types in a multicellular organism
splice the same transcript differently, producing cell type-specific versions of the protein.
[Why does splicing exist?]

Try it yourself: Splice the message

Your mission, should you choose to accept it: decode the following top-secret message. First, remove
the "junk" letters, colored in purple and underlined. Second, put the remaining letters into groups of
three, starting at the beginning.

THEDOGR AMAPQ ANANDA ZAPTQM TETHEHAT

Have you given it a try?

If you remove the purple sequences, you should get this series of letters: [Show result]
If you group the remaining letters into sets of three, you should get this message: [Show result]
The process you just went through is basically what your cells must do when they express a gene. As
we discussed earlier in the article, most eukaryotic pre-mRNAs contain "junk" sequences called
introns, which are like the purple letters in the message. These sequences must be removed, and the
meaningful sequences (exons), equivalent to the maroon letters in the message above, must be stuck
back together to make a mature mRNA.
During translation, the mRNA sequence is read in groups of threeDid
nucleotides.
Each
three-letter
this article
help
you?
"word" corresponds to an amino acid that's added to a polypeptide (protein or protein subunit). If an
RNA hasn't been spliced, it will contain extra nucleotides that itYes
shouldn't, leading to an incorrect
protein "message." Something similar happens if we try to decode the message above without
No
removing the purple letters:

THE DOG R AM APQ ANA NDA ZAP TQM TET HEH AT

Just as removing the purple letters from the sentence is key to ending up with the right message, so
splicing is key to ensuring that an mRNA carries the right information (and directs production of the
correct polypeptide).
[Example using an actual RNA molecule]
[References]

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