HAYWARD, Calif.—Using a sequencing platform that it hopes to introduce commercially by the end of 2005, genetic technology specialist Solexa helped University of Delaware researchers study the small RNA component of the transcriptome, the machinery of gene expression. When more widely applied, the technology may improve the understanding of biological pathways and facilitate drug development.
"The largest problem with identifying the small RNA component is that it requires a huge amount of sequencing due to the fact that some small RNAs are very abundant while many others are extremely rare," says Dr. Christian Haudenschild, Solexa senior manager of technical accounts and co-author of the study, which was published in Science. "So to have an exhaustive survey of the different small RNAs present in a sample, you need to sequence hundreds of thousand of these short molecules."
This effort, he adds, is only economically possible with a technology like Solexa's Massively Parallel Signature Sequencing (MPSS) system. Using MPSS, the researchers identified more than 77,000 small RNAs in the plant Arabidopsis, more than 10 times the number previously identified. The system will work for any organism, however, and Solexa has already processed mammalian and other animal samples using this new application.
For Solexa, this was more than a proof-of-concept effort as it has turned into a new service product for the company.
"Thanks to this new application, MPSS is now available for interrogation of not only mRNA but also the small RNA portion of the transcriptome regardless of which organism one wants to study," Haudenschild says. "The anticipated future release of our next generation of sequencing technology using Sequencing-By-Synthesis will further reduce the cost of these applications."
The collaborative work was a natural extension to earlier interactions between the two groups in National Science Foundations-funded studies on rice and Arabidopsis transcriptomes, Haudenschild says. The capture and sequencing of short RNAs sounded like the ideal application for MPSS as it is able to sequence, in highly parallel fashion, hundreds of thousand of molecules.
"This is the first technology to allow simultaneous identification and quantification of so many small RNAs," says Delaware researcher Dr. Blake Meyers. "With the quantitative data, it's possible to compare tissues or treatments and to identify specific sequences that are regulated. This type of data would otherwise have to be generated using customized microarrays or other approaches, whereas the data were immediately accessible from the MPSS data."
Because of their role in gene regulation and potential as therapeutics, small RNAs, which include microRNAs (miRNAs) and small-interfering RNAs (siRNAs), have garnered increased attention in recent years.
"Several labs have demonstrated that large numbers of human genes are targets of miRNAs and there are at least hundreds of miRNAs in the human genome," says Delaware researcher Dr. Pamela Green. "In RNAi, small RNAs are routinely used to shut off genes of interest to study their function. RNAi also offers the potential for targeting deleterious genes, and researchers are attempting to harness this power for therapeutic purposes."