Intron or Exon?

In many genes, stretches of genetic 'nonsense,' called introns, interrupt the instructions for protein synthesis. Now, a report published in the 11 March online Nature Genetics proposes a new mechanism by which these introns are identified and removed.

When cells produce a new protein, they first copy the appropriate gene into an RNA molecule. Next, the splicing machinery of the cell removes potentially harmful introns and welds together the so-called exons in the gene sequence. Many genetic defects are caused when splicing goes awry and too much is left in or out. This usually happens when the boundaries of introns are mutated beyond recognition for the splicing enzymes. But now a team of scientists led by Francisco Baralle of the International Centre for Genetic Engineering and Biotechnology in Trieste, Italy, has discovered that mutations deep within an intron can also change the way the intron is handled by the splicing machinery.

The team analyzed the DNA of a patient suffering from the neurodegenerative disease ataxia-telangiectasia (A-T). They found that 4 base pairs within intron 20 of the disease-causing gene were missing. But the patient's immune system cells included stretches of a type of RNA, messenger RNA, that were longer than normal, which the researchers demonstrated was caused by the inclusion of the extra intron. In other words, the 4-base-pair deletion within the intron had the surprising effect of turning it into an exon: It was no longer left on the cutting-room floor when the splicing machinery had done its work.

To experiment further, Baralle's group inserted a healthy, 12-base-pair gene sequence that included the 4 base pairs deleted in the A-T patient into an exon of an entirely different gene. Strikingly, the splicing machinery began to treat the whole exon as an intron--the reverse of the previous experiment--and cut it out. The results suggest that this sequence, when functional, helps the splicing enzymes recognize an intron; when absent, as in the A-T patient, it's mistaken for exon material, says Baralle. Baralle suspects that the sequence might control splicing in other genes and could play a role in various diseases, including cancer.

The work marks an "important discovery," says Jim Manley of Columbia University in New York City. Manley thinks that this key sequence deep within introns could be a "stepping stone" that helps the splicing machinery recognize and remove large introns. In the genome at large, there could be "dozens of similar mechanisms" that determine what constitutes an intron, he says.

Related sites
The International Centre for Genetic Engineering and Biotechnology
ISIS: intron sequence and information database
NIH information on A-T
A-T Children's Project