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Alternative splicing in human genes pervasive; may provide clues to new therapeutics
CAMBRIDGE, Mass.—Showing yet again that the human body is even more complicated than people already fear it to be, three separate research studies that appeared online earlier this month from two separate publications—Nature and Nature Genetics—show that alternative splicing of human genes is far more common than previously documented.
The findings, while they may introduce complications by requiring drug discovery and development researchers to consider yet more variable in genomics and proteomics work, may also help lead to better therapies for diseases like cancer, suggests Christopher B. Burge of MIT, senior author of the Nature article, Alternative isoform regulation in human tissue transcriptomes.
"We need to fully understand the spectrum of messenger RNAs and proteins that are produced from our genes, even if it is inconveniently complex," says Burge, an associate professor of biology and biological engineering at MIT. "All of these isoforms are expressed in vivo, and we need to figure out why. And how."
In alternative splicing, a gene is able to produce slightly different forms of the same protein by skipping or including certain sequences from the messenger RNA (mRNA). Nearly all human genes, about 94 percent, generate more than one form of their protein products, Burge's team reports, noting that previous estimates by scientists on the topic of alternative splicing suggested a decade ago that only 10 percent of humans genes did this—a figure that was revised upward to around 50 percent or slightly more in recent years.
"A decade ago, alternative splicing of a gene was considered unusual, exotic," Burge says, "but it turns out that's not true at all—it's a nearly universal feature of human genes."
"One of the applications is that you can discover new mRNA isoforms with the deep sequencing," he continues. "We found over 1,400 high-confidence novel exons with this approach and many thousands of new candidate splice junctions. Being able to say what mRNA species are present in an unbiased way without having to make guesses in advance is something that you can't really do with microarrays."
Also, finding new isoforms could mean finding more markers for cancer and other diseases.
"If you think about an application like the expression and classification of tumor types, if you can look at mRNA isoform expression specifically instead of just gene expression, you get a richer set of features which should help to improve classification," Burge notes. "Another application of course is that the protein isoforms encoded by these new mRNA isoforms might have activities that are therapeutically useful."
One of the reasons it hasn't been clear that such an overwhelming majority of human genes do alternative splicing, Burge says, is because it's only recently that the cost of sequencing and discriminating similar mRNA isoforms using microarrays has become affordable enough to study isoforms on a genome-wide scale. The MIT team took mRNA samples from 10 types of tissue and five cell lines from a total of 20 individuals, and generated more than 13 billion base pairs of sequence, the equivalent of more than four entire human genomes, according to MIT reports.
In one of the Nature Genetics papers, Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing, Canadian researchers used a combination of mRNA-Seq and EST-cDNA sequence data to investigate splice junctions in six human tissues. They, uncovered new splice junctions in roughly 20 percent of multi-exon genes and estimated from their finding roughly 95 percent of gene transcripts undergo alternative splicing, a number just a hair higher than MIT's estimate.
Researchers at Seattle's Rosetta Inpharmatics and elsewhere added to the pile of alternative splicing insights with the article, Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines, when they used whole-transcript custom microarrays to look at genome-wide expression of alternative splicing events in nearly 50 human tissue and cell line samples. Their work led to the discovery of more than 140 motifs predicted to regulate alternative splicing. DDN