Splicing
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[edit] Introduction
You should recall that the process of protein synthesis in a cell requires the transcription of DNA into messenger RNA (mRNA) followed by the translation of the mRNA into protein. Other, rarer RNA, such as tRNA and rRNA, don't get transcribed into protein, but play a direct role in the cell as functional RNA. The reader who does not recall any such thing should read our article on DNA before trying to tackle this article.
In between the process of transcription and whatever role the RNA plays in the cell, the RNA may have pieces snipped out of it, the remaining RNA being joined back together to form a continuous strand. The bits that are snipped out of the RNA are called introns, the process of snipping out introns and reconnecting the RNA is called splicing, and the bits of RNA that are separated by introns, and are present in the mature RNA (that is, the RNA after splicing) are called exons.
The words "intron" and "exon" are also used to describe the corresponding sections of the DNA: that is, a section of DNA that is transcribed as an intron to be snipped out of the RNA is also referred to as an intron.
Hence, a gene consists of a string of alternating introns and exons. A gene may have no introns; it may have dozens. In eukaryotic organisms (i.e. organisms whose cells have nuclei, such as plants and animals) the typical gene consists mostly of introns. An average protein-coding gene will be about 8000 nucleotides long, whereas a average piece of mature mRNA after splicing will only be 1200 nucleotides long (figures from Campbell and Reece, Biology).
[edit] How
Group 1 introns are self-splicing: they pinch themselves out of the mRNA, just as a result of the chemistry of the sequence of bases in the intron. For this they require only the assistance of a single ribonucleotide of RNA with a guanine base. Obviously these are abundant in the cell, hanging around waiting to be strung together into RNA: so despite needing assistance, Group 1 introns are still described as self-splicing, because no special bit of cellular machinery needed to evolve for them to self-splice: they do so just as a result of their sequence of bases and the fact that the cell has lots of ribonucleotides floating about in it. [1]
Group 2 introns are also self-splicing, with no assistance whatsoever: purely as a result of the sequence of bases in the RNA, they curl themselves up and snip themselves out of the RNA, with the excised intron ending up in what is known as a lariat structure --- a loop of RNA with a tail.[2]
However, the most important sort of introns are nuclear introns, which, as the name suggests, are found only in organisms that have cells with nuclei. Indeed, the importance of nuclear introns is such that in some resources you will see introns being discussed as though all introns were nuclear introns. Nuclear introns are far from being self-splicing: rather, they are spliced with the aid of a rather complicated bit of cellular machinery called a spliceosome (see the diagram to the right).
As with Group 2 introns, nuclear introns end up curled up in a lariat structure. This suggests a pathway for the evolution of nuclear introns and the spliceosome, beginning with self-splicing introns, progressing by the addition of cellular machinery that makes the process more reliable and efficient, and ending up with introns that can't splice without assistance.
The spliceosome varies from species to species more than is usual in an important part of the cellular machinery, sometimes in ways that give tantalising glimpses into its evolutionary history. For example, the protein known as SPF45 has a role in repairing DNA in plants; but in animals it performs a dual role, assisting in DNA repair and also assembling with the other components to form part of the spliceosome.[3]
The typical process of splicing nuclear introns is shown in the video below. This movie shows the splicing of a "U2 type" intron; there are also "U12 type" introns, which are spliced by a different structure known as the minor spliceosome. In both cases the result is that the intron gets snipped out of the RNA and a lariat structure is formed.
[edit] Why?
The obvious question is: what are introns for? In the case of nuclear introns, we have some rather complicated cellular machinery (the spliceosome) to make sure that intons don't get translated into protein. One seemingly obvious alternative would be to have no spliceosome and no nuclear introns, which would be simpler. In fact, they play a number of roles, which we shall review below.
Protein domains correlate strongly with exons[4], as shown in the diagram to the left.
[edit] Recombination and mutation
The separation, by introns, of regions of DNA coding for different domains of a protein has a couple of useful evolutionary consequences.
First, because most of a gene consists of introns, this means that if recombination involves crossing-over in mid-gene, it probably won't involve crossing over in mid-exon. So recombination will produce a new assortment of intact exons corresponding to protein domains, which is more likely to be successful.
By analogy, imagine you have two computers systems, each consisting of a printer, monitor, keyboard, the system unit, et cetera, of different makes. You are far more likely to find a new and better configuration by switching around these entire units of the computers, swapping round the monitors, or the modems, and so forth, until you find an optimal setup, then by swapping around the electronic components within the various units, taking a bit out of one monitor and putting it into a monitor of a different make. Biological systems are of course more robust than electronic gadgetry, but this analogy roughly conveys the idea.
The same effect also makes it more probable that a small translocation or duplication of one bit of a gene into another will produce a useful or at least a harmless result.
[edit] Alternative splicing
Another advantage of introns is that they open up the possibility of splicing the same primary transcript more than one way, treating regions of the primary transcript as introns or exons on a conditional basis.
For example, in the human gene for cardiac troponin T, the splicing depends on the state of development --- in a fetus, exon 5 is left in the mRNA; in adults, it is treated as an intron and snipped out.
Or consider the calcitonin gene. The splicing of the RNA depends on the sort of cell in which it's expressed. In the thyroid, it's spliced one way, so that the final protein product after translation is calcitonin; in the brain, the RNA is spliced another way, so that it produces CGRP ("calcitonin gene related peptide").[5]
In fruit flies, there is alternative splicing dependent on the sex of the fly. As you can see, then, there are a number of different conditions that can affect splicing, some of which may yet be unknown: for example, we are unaware of any case where alternative splicing is dependent on temperature, but we should not be at all surprised to learn of an instance of this.
The existence of alternative splicing explains what would otherwise be something of a puzzle. You may remember reading in the news that when scientists sequenced the human genome, they found fewer genes than they expected: and one reason that they were expecting more is that they already knew that there were more proteins than the number of genes they counted. This is readily explained by the alternative splicing of genes; in fact, there is evidence that most human genes that have introns are alternatively spliced[6].
[edit] Selfish DNA
Some introns may also be, to some extent, selfish DNA. Consider what happens when a translocation adds an intron to a gene, or an insertion increases the length of an existing intron. Because the intron is going to be removed from this transcript, this shouldn't affect protein function.
It will come at a slight cost to the organism, because it adds nucleotides to the DNA that have to be copied in DNA replication; and also it adds ribonucleotides to the mRNA that gets transcribed, and these processes have a metabolic cost. However, considering the vast number of nucleotides already being copied and transcribed, the difference is minimal, and this cost would be almost invisible to natural selection. Such near-neutral mutations can therefore survive in the gene pool, and may go on to be fixed in the gene pool by genetic drift.
Note that these explanations of the role of introns are not exclusive: some introns facilitate alternative gene splicing, some introns, although not alternatively spliced, may still enhance the outcomes of recombination by dividing the gene into exons coding for domains, and some may be there for no particular reason except that natural selection permits it.
