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With a Little Help From the NSF, Cold Spring Harbor Laboratory Launches RNAi Initiatives

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With a staff that includes researchers such as Greg Hannon and Rob Martienssen, it’s not too surprising that Cold Spring Harbor Laboratory would be the source of two new ambitious RNAi projects.

With the help of National Science Foundation funding, CSHL has begun two grant projects looking to develop tools for high-throughput RNAi in plants, and to expand university students’ access to the gene-silencing technology.

The first project, which is being headed up by Hannon, is entitled “Development of Tools for High-Throughput RNA Interference in Plants,” and aims to “lay the groundwork for rapid generation of genome-scale resources for triggering post-transcriptional gene silencing of plant genes,” according to the grant’s abstract.

“As the scientific community progresses toward the completion of genome sequences, the availability of genome-scale tools for investigating gene function becomes critical,” the abstract notes. “Of course, conventional mutagenesis and genetics will always be a mainstay of such efforts; however, more directed tools that selectively attack the expression of genes in a targeted fashion would accelerate reverse genetic approaches to understanding the function of genes and gene families.”

The development of RNA interference as a tool has made this type of selective gene expression possible, the abstract states. Genome-scale projects are underway in worm, fly, and human systems, it adds, and the grant project is looking to develop resources to help researchers do the same in plants.

“Flexible vectors will be developed that incorporate short and long hairpin RNAs and their efficacy will be tested in plant cell cultures and intact plants,” the abstract states. “The optimized vectors will be made available, as well as silenced plants. The long-term goal is to use these vectors to develop genome scale RNAi libraries for plants in a rapid and cost-effective way.”

Initially, the project will use tobacco and Arabidopsis as model systems. Once the RNAi work is validated in these plants, the researchers will begin applying the technologies in rice. Vectors resulting from the effort will be distributed through Open Biosystems, which sells human and mouse shRNA libraries developed by Hannon’s lab, while plant materials will be made available from CSHL.

The grant project, which has thus far received about $200,000 in NSF funding, began in September 2004 and will run through February 2006.

The second project, entitled “Developing and Disseminating New Laboratories in RNAi and Functional Genomics,” is focused on establishing modules “of investigative laboratories and bioinformatics exercises that engage students in the new technologies of RNA interference and computer-based genome analysis,” according to the grant’s abstract.

“Over the past 15 years, many laboratories have been implemented that illustrate basic concepts of microbial and molecular genetics,” the abstract states. But the completion of the Human Genome Project “challenges teachers to move laboratory instruction to a higher level of biological integration: the functional analysis of genes and proteins in eukaryotic organisms.”

RNAi experiments in C. elegans have proven to be both extremely effective in studying gene function, while being “simple and robust enough to join bacterial transformation and gel electrophoresis as a mainstay of the college teaching laboratory,” the abstract notes. Furthermore, once the basics of RNAi are learned, students who have access to the proper resources are able to design their own experiments using the technology to examine C. elegans gene function.

To help set up the modules, CSHL is working with faculty at two- and four-year colleges and the Dolan DNA Learning Center, which is an operating unit of the institute focused on educating the public about genetics, the abstract states.

“Newly developed modules will be introduced to and critiqued by biology faculty and high school biology teachers at workshops held at a variety of sites around the nation,” it adds. “Instructional and bioinformatics resources developed in this project will be disseminated via [Dolan’s website], Cold Spring Harbor Laboratory Press, and Carolina Biological Supply Company.”

This grant project, which began in June 2004 and will wrap up in May 2006, and has to date received about $295,611 from the NSF. It is also running in parallel with a third NSF-funded effort organized by Micklos focused on developing a lab and Internet-based plant research curriculum for students.

Under this project, entitled “Developing and Disseminating New Laboratories on Plant Molecular Genetics and Genomics,” laboratories use Arabidopsis and various food crops to “illustrate key concepts of gene and genome analysis, including the relationship between phenotype and molecular genotype, genetic modification of plants and detection of transgenes in foods, and linkage and bioinformatic methods for gene mapping,” the grant’s abstract states. Meanwhile, students have the opportunity to assist CSHL researchers in analyzing Arabidopsis genes of unknown function.

The labs are to be supported by a website that provides online protocols, custom analysis tools, shared databases, collaborative bulletin boards, and chat systems, the abstract notes.

“The [proposed project] is comprised of an initial development phase, culminating in a focus workshop of faculty advisors drawn from two- and four-year colleges representing six regions of the United States,” the abstract states. “During the dissemination phase, faculty advisors will organize weeklong training workshops to reach 144 instructors.”

Applied Biosystems, Bio-Link National Center for Advanced Technological Training in Biotechnology, Carolina Biological Supply Company, and Cold Spring Harbor Laboratory Press said they will help the effort, it adds.

This project began in February 2003 and will end in January 2006, and has received nearly $500,000 from the NSF to date.

— DM

 

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