Alternative Splicing Goes Mainstream

[iansmith]

Multilayered regulatory mechanisms at the RNA level increasingly show their stuff | By Sam Jaffe

In eukaryotic genetics, the one-gene/one-protein concept has, for the most part, breathed its last. Researchers have rallied behind mechanisms such as alternative splicing, which may allow a lowly 30,000-gene genome to produce the dizzying variety of proteins that some believe is necessary to produce beings as complex as humans.

Alternative splicing--the post-transcriptional editing process that can result in various mRNAs--was previously seen as an interesting but relatively uncommon sideshow to the big-tent events covered in central dogma: DNA begets RNA begets protein. Now, thanks to a wave of new bioinformatics databases, techniques, and studies, alternative splicing has emerged as not only pervasive, but perhaps as a central regulatory mechanism. And it may not be alone. A previously unnoticed glut of premature stop codons in usable exons suggests a larger role for RNA decay mechanisms previously associated with quality control. Cousins such as alternative polyadenylation might play a similar role. These processes could band together as part of a vast regulatory network, controlling everything from developmental programs and cell differentiation to housekeeping functions and circadian rhythms.

At the heart of this theory is a reassessment of how the gene-to-protein process works, especially with the confounding riddle of how a mouse and a human being can be so different, even though both have about 30,000 genes. "Thirty thousand genes are probably enough," says Miles Wilkinson of the M.D. Anderson Cancer Research Center in Houston. "The question isn't how many genes or even how many proteins, but how the regulatory system works to control the machinery. The regulatory system is probably far more complex than we ever imagined."

MORE THAN A STOREHOUSE Such talk lends credence to John Mattick's theory of genetic regulation. Mattick, director of the Institute for Molecular Bioscience at the University of Queensland in Brisbane, Australia, has argued vociferously that nonprotein-coding RNA (including microRNAs, siRNAs and intronic RNA) are part of a vast multitasking regulatory mechanism. He points out that the intron-sparse yeast genome and the seemingly junk-dense human sequence are very similar. What differentiates them are the vast intronic regions shared by humans and other complex organisms. Mattick outlined his controversial theory in a paper published in 20011 in which he wrote, "The majority of phenotypic variation between individuals (and species) results from differences in the control architecture, not the proteins themselves."

Probably an important cog in that as-yet-undefined regulatory system is the alternative splicing mechanism. Most genes contain at least one position for alternative splicing where the spliceosome can choose one of several alternative splice sites. Each splice variant mRNA may then code for a different protein. Alternative splicing is also seen as a method for enhancing evolutionary adaptability in an organism. "It's like a big storehouse of potential genetic information," says Douglas Black, a Howard Hughes Medical Institute investigator at the University of California, Los Angeles. "It's a mechanism that allows testing a new mutation without losing the wild-type version."

Research shows that alternative splicing is far more pervasive than previously thought, perhaps too pervasive to be simply an evolutionary warehouse. In 1998, Peer Bork's group at the European Molecular Biology Lab in Heidelberg, Germany, mapped expressed sequence tags (ESTs) to human cDNAs and unexpectedly found that the observed putative splice variants exceed the 5% prediction offered by Nobel laureate Philip Sharp,2 one of the original discoverers of mRNA splicing. In 2001, they expanded the study to seven eukaryotic species and found that almost half the genes in animals could have alternative splice sites.3

Now, Bork says that even a prediction of 45% is a significant underestimate, based on his and others' work. "The best figure now is [that] somewhere around 60% of genes use alternative splicing," he says, referring to work done by Christopher Lee at UCLA.4 "That number has been increasing steadily at a linear rate in the last few years." One recent study, he points out, hints that almost all highly expressed genes use alternative splicing.5

Just as Bork's work seems to have proposed a solution to the genetic complexity question (that alternative splicing accounts for all those proteins), it also confounds the theory that humans owe their complexity to more alternative splicing in their genome. Other so-called lower species aren't very far behind in the preponderance of alternative splice sites. About 35% of murine ESTs showed them, as did at least 15% of Caenorhabditis elegans ESTs. When normalized, says Bork, the data for these organisms show similar splicing frequency to humans, meaning that alternative splicing by itself may not be enough to explain why humans drive cars and roundworms squirm in the dirt.

http://www.the-scientist.com/yr2003/dec/research2_031215.html

 

[selfAdjoint]

Wow!

Do I understand correctly that these new functions come into play upstream of messenger RNA? So the new chain would be DNA+Introns => lots of control functions => much tailored mRNA => any of a number of different proteins from the same DNA?

 

[iansmith]

It is not exactly like you described. Its splicing site which are specific sequence can be target by the splicesome in a given cellular state. The mRNA is intron and exon. The splicing removes the introns and keeps the exons. The difference is that some exons migth be reject for a certain function but kept for another function. As you said you get many tailored made processed mRNA which in term increase the potential number of protein.

 

[Monique]

Upstream of mRNA is a region called the 3'UTR (untranslated region) which plays a role in regulating the translation of the sequence.

 

[selfAdjoint]

Is there any account of this that gives some detail but is accessible to a general reader?