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R E S E A R C H Alternative splicing and the proteome
P R O F I L E
transcriptional activation when the repression domain is gone,” says Lee. Other Pbx family members also have Until recently, researchers have viewed isoforms that lack this region, which splicing merely as a way to get rid of increases transcription of the genes they noncoding junk (introns) from mRNAs. regulate. It is becoming increasingly clear, howLee explains that the case studies ever, that splicing can also remove or highlight broad themes that the reinsert various coding regions (exons), searchers observed throughout their sometimes producing hundreds or bioinformatic analyses of ASP database thousands of alternative transcripts entries. Alternative splicing appears to from a single gene. Alternative splicing, have functional consequences, which says Christopher Lee of the University of can include changing where a protein is California, Los Angeles, can result in localized or altering its interactions with protein isoforms with different funcDNA or with other proteins. tions, depending on which exons are According to Lee, the present. ASP database will be a This is a new way ATG (a) II III IV V VI VII VIII IX I great resource for bioloof thinking for those Genomic gists and biochemists. “We who study gene II III IV V VI VII VIII IX hope that biologists will expression, says Lee. I (b) Pbx2a mRNA go in and mine these new Whereas transcripProtein C N protein forms that we’re tional regulation, for Poly-A Homeobox Repression domain reporting and [perform] instance, increases or II III IV V VI VIII experiments [to] figure out decreases the total IX I Pbx2b mRNA what these changes are number of transcripts doing functionally,” he made, “alternative Protein N C Poly-A Homeobox says. Researchers who are splicing changes the not experts in the splicing architecture of a pathAlternative splicing. (a) Schematic of the PBX2 gene. (b) Two alternative mRNAs and field will especially benefit way by removing key proteins of PBX2. The Pbx2b protein isoform lacks exon VII and exon IX, which is the transcription repression domain. from Lee’s work. “Historiinteractions—links— cally, it has not been easy inside that network,” to make use of alternative splicing inforthe frequency that a particular domain he says. mation for someone who mainly works was removed. According to Lee, “On Lee’s field is benefiting greatly from on a protein’s function,” he says. “You average, about one [domain] in ten is ongoing sequencing efforts. “The big couldn’t translate very easily from [EST observed to be removed by some alterchange in the alternative splicing field is data] to what the consequences would native splicing event within ASP.” But he coming from genomics, specifically EST be for the protein, so that’s one connecsays that some coding sequences, such [expressed sequence tag] sequencing tion we’ve tried to bridge with our ASP as the annexin domain, are removed and now also microarrays, where there database.” much more often. are massive amounts of alternative Although the research team has Four case studies are presented in splicing being discovered,” says Lee. already accomplished a great deal, Lee which the researchers analyze a set of “[We are attempting] to use that says many intriguing questions remain. isoforms from one gene. For example, a genomics data to infer the impact on He is currently pursuing the link novel isoform of the transcriptional regthe proteome.” between splicing and evolution, for ulator Pbx2 was identified in which a In this issue of the Journal of Proinstance. “We’ve separately published a protein-interaction domain, which is teome Research (pp 76–83), Lee and his paper about [how] alternative splicing known to bind to two co-repressors, was colleagues undertake the difficult task of may accelerate the rate of creation and missing. The researchers suggest that determining protein isoform sequences loss of new exons during the course of this isoform would completely change from mRNAs and ESTs, which are evolution,” he says. “It may provide a the activity of Pbx2. “You can think of it cDNAs made from segments of mRNAs. mechanism for being able to alter and as a switch mechanism, where you They compiled 13,384 alternatively build new components of protein strucswitch the consequences of Pbx2 bindspliced protein forms (ASPs) from ture and function.” ing to its target DNA from repression human genes and entered them into a —Katie Cottingham when the repression domain is there to new free database.
© 2004 American Chemical Society
The researchers studied the effect of alternative splicing on protein function. By referring to two other databases that contain functional domain information, they identified the parts of each protein likely to be involved in its activity. Most alternative splicing events, says Lee, remove most or all of a functional domain from the major, or most abundant, isoform. To see if some types of domains are preferentially excised, Lee and colleagues examined the rate of domain removal throughout all of the proteins in their dataset and compared that to
Journal of Proteome Research • Vol. 3, No. 1, 2004
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