Alternative splicing



Alternative splicing is the variation of the splicing process in which the exons of the primary gene transcript, the pre-mRNA, are arranged in alternative ways. pre-mRNAs which have been transcribed from the same gene are separated and reconnected in different ways to yield various mRNAs. These mRNAs then are translated into proteins, which can differ from one another enormously in their function.

When the pre-mRNA has been transcribed from the DNA, it includes several introns and exons. (In nematodes, the mean is 4-5 exons and introns; in the fruit fly Drosophila there can be more than 100 introns and exons in one transcribed pre-mRNA.) But which introns and exons will eventually be included in the mRNA is not yet determined at this stage. This decision is made during the splicing process. The regulation and selection of splice sites is done by Serine/Arginine-residue proteins, or SR proteins. The use of alternative splicing factors leads to a modification of the definition of a "gene". Some have proposed that a gene should be considered as a twofold information structure:
 * A DNA sequence coding for the pre-mRNA
 * An additional DNA code or other regulating process, which regulates the alternative splicing.

There are four known modes of alternative splicing:
 * Alternative selection of promoters: this is the only method of splicing which can produce an alternative N-terminus domain in proteins. In this case, different sets of promoters can be spliced with certain sets of other exons.
 * Alternative selection of cleavage/polyadenylation sites: this is the only method of splicing which can produce an alternative C-terminus domain in proteins. In this case, different sets of polyadenylation sites can be spliced with the other exons.
 * Intron retaining mode: in this case, instead of splicing out an intron, the intron is retained in the mRNA transcript. However, the intron must be properly encoding for amino acids.  The intron's code must be properly expressible, otherwise a stop codon or a shift in the reading frame will cause the protein to be non-functional.
 * Exon cassette mode: in this case, certain exons are spliced out to alter the sequence of amino acids in the expressed protein.

Splicing mechanism
The intron consists of GU at 5' end and AG at 3' end, with a branch site (A) in the middle and a (py)n, denoting the polypyrimidine tract prior to the 3' end. When splicing starts, the branch site A attacks the 5' end G to form a 2',5'-phosphodiester linkage. Then the 3' end of upstream exon (G) captures the 3' end of intron by forming phosphodiester bond again, so that two exons are joint together, leaving a free intron in lariat form. In mRNA splicing, snRNPs are involved, namely, U1 to U6. For example, when splicing mRNA, U1 binds to 5' GU and U2 binds to branch site (A), then U4,U5,U6 complex comes, and U6 replaces the U1 position. U1 and U4 leaves, then U2 and U6 associate to form the lariat intron, and U5 helps bring the upstream and downstream exons together. U3 is not involved in mRNA splicing.

Importance in molecular genetics
Alternative splicing is of great importance to genetics - it invalidates the old theory of one DNA sequence coding for one polypeptide (the "one-gene-one-protein" hypothesis). External information is needed in order to decide which polypeptide is produced, given a DNA sequence and pre-mRNA. (This does not necessarily negate the central dogma of molecular biology which is about the flow of information from genes to proteins). Since the methods of regulation are inherited, the interpretation of a mutation may be changed.

It has been proposed that for eukaryotes it was a very important step towards higher efficiency, because information can be stored much more economically. Several proteins can be encoded in a DNA sequence whose length would only be enough for two proteins in the prokaryote way of coding. Others have noted that it is unnecessary to change the DNA of a gene for the evolution of a new protein. Instead, a new way of regulation could lead to the same effect, but leaving the code for the established proteins unharmed.

Another speculation is that new proteins could be allowed to evolve much faster than in prokaryotes. Furthermore, they are based on hitherto functional amino acid subchains. This may allow for a higher probability for a functional new protein. Therefore the adaptation to new environments can be much faster - with fewer generations - than in prokaryotes. This might have been one very important step for multicellular organisms with a longer life cycle.

A common myth is that alternative splicing is responsible for humans supposedly being the most complex animals, saying that humans perform more alternative splicing than the other animals. However, this is not the case. A study conducted on the subject found that "the amount of alternative splicing is comparable, with no large differences between humans and other animals." The "record-holder" for alternative splicing is actually a Drosophila gene called Dscam, which has 38 000 splice variants.