The July 9, 2008, issue of Nature provides a reminder that despite that fact that much attention is focused on the deluge of novel RNA types being discovered, older forms of RNA have not yielded all their secrets either. Researchers from UC Santa Cruz reported discovering so-called hammerhead ribozymes in the mammalian genome.
Hammerheads ribozymes are a form of regulatory RNA named for their shape when they are folded up. But their mechanism of action also sounds a bit like a shark taking a feeding frenzy too far. Hammerheads inhibit transcription when they are part of an RNA sequence by essentially cutting themselves into two pieces, effectively turning off the gene expression by preventing protein translation.
Hammerheads were first discovered in plant viruses, and also had been found in some amphibians and insects, first author Monika Martick, a postdoctoral researcher at UC Santa Cruz, told BioWorld Today. But "although the sequence is quite simple, there had been no known functional hammerheads in mammals."
Martick and her colleagues changed that by searching genome databases in a way that allowed them to see fragments of hammerhead coding sequence that were at a distance to each other, rather than contiguous.
Using that method, they found hammerhead parts separated by inserts of up to 1,700 base pairs in the CLEC2 gene of several mammal species, including mice, rats, horses and platypuses. Martick said that because they appear to be conserved, she and her colleagues believe that the intervening sequences themselves play a part in the hammerhead's functions, though thus far, they do not know what that function might be.
Cell culture experiments showed that the messenger RNAs containing the embedded sequences form an active ribozyme, and that ribozyme decreases the activity of the CLEC2 gene in mammalian cells.
To date, Martick and her colleagues have not found any hammerhead ribozymes in humans. She said it was unclear why. One possibility is that such structures do not exist in humans, but it also is possible that with more knowledge about hammerhead sequences, they will be uncovered in the human genome as well.
Regardless of whether hammerheads exist naturally in humans, some researchers are attempting to use hammerhead structures to control human genes. Because of the potential diversity of their sequences, and because any gene with a hammerhead ribozyme embedded within it is not expressed in the default state, some scientists hope that using genes with embedded ribozymes could be useful in improving the safety of gene therapy. (See BioWorld Today, Oct 4, 2004.)
If hammerhead ribozymes exist naturally in humans, then they could be targeted to activate the genes they inhibit by the same principle that is being explored for gene therapy. Martick said she thinks that if hammerhead ribozymes are discovered in human genes, they could "absolutely" be targeted therapeutically, especially given that the CLEC2 gene, which is important in both immune system function and bone metabolism, could have direct therapeutic relevance itself. "These genes are quite important," she said. "In some cases, they have to be expressed."
For them to be expressed, the activity of the hammerhead has to somehow be prevented.
Though the researchers have not yet identified one, they are confident that such an "off switch" exists for the mammalian hammerhead. Identification of such an off switch also could be useful; one of the challenges of using hammerhead ribozymes to control gene activity in gene therapy research has been that compounds to inhibit the ribozyme's self-cleavage can be tough to find.