UCSF creates fast, affordable tool for finding gene 'on-off' switches

May 19, 2009

UCSF scientists have created a method of quickly identifying large numbers of the genetic material known as short hairpin RNA — also called shRNA - that turns genes on and off.

The method, which the research team has used to create a library of 22,000 of these "on-off" switches for roughly 600 human , provides a tool for scientists throughout the world, with ultimate impacts on the study of the genetic basis of diseases ranging from HIV to high cholesterol, Parkinson's disease or cancer. The team is currently working on creating an shRNA library for the entire human genome.

Findings are available in the Advanced Online Publication section of the journal at http://dx.doi.org/10.1038/nmeth.1330 and will appear in the June 2009 print issue of the journal.

Since their discovery in the past decade, biologically active small RNAs have become the holy grail of much pharmaceutical and genomics research, offering the hope of creating targeted therapeutics to "turn off" or turn down the "volume" of various genes involved in disease, according to Michael McManus, PhD, a UCSF microbiology professor and senior author on the paper. This process is known as .

Until now, however, the process of finding shRNAs that are able to potently deactivate a given gene has been extremely laborious and laden with many false results.

The new method uses a microarray technology to generate large numbers of these shRNA strands for each target gene - roughly 10 times the volume of traditional methods - thereby enabling researchers to screen for interference much faster than before and at a minimal cost, McManus said.
"This means that even a small laboratory with limited resources can perform complex genetic screens on mammalian cell cultures," he said. "With the current scarcity of research funding, these are invaluable tools for researchers worldwide."

Many diseases already have been linked to specific genes that are mutated or turned on to cause the illness. How those genes actually cause the illness is less clear, but by using shRNA to turn the genes off, researchers can study specific genetic function and start to identify drugs or therapeutics to change it.

The system, which uses "deep sequencing" technology to rapidly uncover effective shRNAs by simultaneously sequencing millions of base pairs of DNA, also enables scientists to better identify which of those tiny RNA-strands is most effective in turning off a particular gene and which ones are effective but also cause side effects on untargeted genes.

Research into gene function has been done for years with worms and fruit flies, whose short life spans and rapid reproduction make genetic testing relatively inexpensive, McManus said. But in mammals, studying the function of individual genes can often cost a laboratory $100,000 or more in basic materials and require complex technology to run.

The UCSF shRNA library aims to offer more than 600,000 different samples of shRNA - roughly 30 for every human gene. Once the shRNA library is complete for the , the team will continue creating libraries for other species.

McManus said he plans to make shRNA libraries available through the UCSF Sandler Lentiviral RNAi Core, which he directs. The Core provides essential equipment, training, supervision, and monitoring for researchers working in lentiviral-based research, as well as offering viral packaging and other services for researchers.

Source: University of California - San Francisco

Explore further: Japan lab unable to replicate 'stem cell' findings

add to favorites email to friend print save as pdf

Related Stories

Team demos safety of RNA therapy

Sep 26, 2007

Researchers from MIT, Alnylam Pharmaceuticals and other institutions have demonstrated the safety of a promising type of genetic therapy that could lead to treatments for a wide range of diseases such as cancer.

Team identifies 13 new tumor-suppressor genes in liver cancer

Nov 18, 2008

Over the years, hunting for cancer-related genes and understanding how they work has been an important, although time-consuming, exercise. At Cold Spring Harbor Laboratory (CSHL), five different research groups have now combined ...

Weakened RNA interference reduces survival in ovarian cancer

Dec 17, 2008

Levels of two proteins in a woman's ovarian cancer are strongly associated with her likelihood of survival, a research team led by scientists at The University of Texas M. D. Anderson Cancer Center reports in the Dec. 18 ...

Team develops safe, effective RNA interference technique

Apr 28, 2008

A team of researchers from MIT and Alnylam Pharmaceuticals has developed safe and effective methods to perform RNA interference, a therapy that holds great promise for treating a variety of diseases including ...

Recommended for you

Researchers film protein quake for the first time

4 hours ago

One of nature's mysteries is how plants survive impact by the huge amounts of energy contained in the sun's rays, while using this energy for photosynthesis. The hypothesis is that the light-absorbing proteins ...

Deploying exosomes to win a battle of the sexes

Aug 25, 2014

There are many biological tools that help animals ensure reproductive success. A new study in The Journal of Cell Biology provides further detail into how one such mechanism enables male fruit flies to imp ...

User comments : 0