Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New resource makes gene-editing technology even more user friendly

16.07.2015

Researchers at Harvard University and the University of California, San Diego, have developed a new user-friendly resource to accompany the powerful gene editing tool called CRISPR/Cas9, which has been widely adopted to make precise, targeted changes in DNA. This breakthrough has the potential to facilitate new discoveries in gene therapies and basic genetics research. The research was published in the July 13 issue of Nature Methods.

The study describes an approach to simplify a laborious part of the gene editing process using the CRISPR/Cas9 system: choosing the best components to match specific gene targets.


CRISPR/Cas9 is a gene-editing tool that can target a particular segment of DNA in living cells and replace it with a new genetic sequence.

Credit: Jacobs School of Engineering/UC San Diego

"We've taken a step towards making the CRISPR/Cas9 system more robust," said Prashant Mali, an assistant professor in the Department of Bioengineering at the UC San Diego Jacobs School of Engineering, and a co-first author of the study.

CRISPR/Cas9 is a relatively new genome engineering tool that can target a particular segment of DNA in living cells -- such as a gene mutation -- and replace it with a new genetic sequence. This technology ultimately has applications in gene therapies for genetic disorders such as sickle cell anemia and cystic fibrosis.

The CRISPR/Cas9 system has two components: a short "guide RNA" with a sequence matching a particular gene target, and a large protein called Cas9 that cuts DNA precisely at that target. Herein lies the beauty of the CRISPR/Cas9 system: to target another region of the genome, researchers can simply change the guide RNA sequence to match the new gene target.

However, finding the best guide RNA match for a specific gene target is a labor-intensive process. This is because multiple guide RNA sequences can serve as potential matches for each gene target. As a result, researchers might need to test numerous candidates of guide RNAs before finding the most active guide RNA.

Matchmaking software for faster guide RNA selection

To decipher what makes certain guide RNAs better than others, the team conducted what they called a "library-on-library" approach, in which they evaluated a library containing thousands of guide RNAs against a library containing thousands of corresponding gene targets.

The team analyzed the data from the library-on-library approach to determine patterns among the guide RNAs that were the most active. Using the data and patterns from these thousands of gene targeting experiments, the team developed a new matchmaking software that predicts and ranks the best guide RNA matches for any given gene target.

"From these experiments, we were able to find features in the guide RNAs that worked and in those that didn't work. We built a computational model that accounts for all these different features. The end product is an interactive software for users to find guide RNAs that are predicted to be highly specific and highly active for their gene targets," said Raj Chari, a research fellow working in the lab of Professor George Church in the Department of Genetics at Harvard Medical School, and a co-first author of the study.

"We hope to minimize the time and work in finding the most successful guide RNA sequence for a gene target, which will be helpful for finding new gene therapies," said Chari.

"Overall, this new method offers a simple approach to assess a large number of guide RNAs in a short amount of time. We believe this will be a useful resource for the community towards designing improved genome engineering experiments," added Mali.

This work was supported by the National Institutes of Health (grant P50HG005550), a Banting Fellowship from the Canadian Institutes of Research, University of California San Diego startup funds, and a Burroughs Wellcome Career Award.

Full paper:

"Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach" Nature Methods 2015, published July 13.

Author list:

Raj Chari and George M. Church, Department of Genetics, Harvard Medical School, Boston, MA; Prashant Mali, Department of Bioengineering, UC San Diego, La Jolla, CA; Mark Moosburner, Scripps Institute of Oceanography, UC San Diego, La Jolla, CA.

Media Contact

Liezel Labios
llabios@ucsd.edu
858-246-1124

 @UCSanDiego

http://www.ucsd.edu 

Liezel Labios | EurekAlert!

Further reports about: Bioengineering CRISPR Cas9 DNA RNA RNA sequence sequence specific gene

More articles from Life Sciences:

nachricht Fine organic particles in the atmosphere are more often solid glass beads than liquid oil droplets
21.04.2017 | Max-Planck-Institut für Chemie

nachricht Study overturns seminal research about the developing nervous system
21.04.2017 | University of California - Los Angeles Health Sciences

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Deep inside Galaxy M87

The nearby, giant radio galaxy M87 hosts a supermassive black hole (BH) and is well-known for its bright jet dominating the spectrum over ten orders of magnitude in frequency. Due to its proximity, jet prominence, and the large black hole mass, M87 is the best laboratory for investigating the formation, acceleration, and collimation of relativistic jets. A research team led by Silke Britzen from the Max Planck Institute for Radio Astronomy in Bonn, Germany, has found strong indication for turbulent processes connecting the accretion disk and the jet of that galaxy providing insights into the longstanding problem of the origin of astrophysical jets.

Supermassive black holes form some of the most enigmatic phenomena in astrophysics. Their enormous energy output is supposed to be generated by the...

Im Focus: A Quantum Low Pass for Photons

Physicists in Garching observe novel quantum effect that limits the number of emitted photons.

The probability to find a certain number of photons inside a laser pulse usually corresponds to a classical distribution of independent events, the so-called...

Im Focus: Microprocessors based on a layer of just three atoms

Microprocessors based on atomically thin materials hold the promise of the evolution of traditional processors as well as new applications in the field of flexible electronics. Now, a TU Wien research team led by Thomas Müller has made a breakthrough in this field as part of an ongoing research project.

Two-dimensional materials, or 2D materials for short, are extremely versatile, although – or often more precisely because – they are made up of just one or a...

Im Focus: Quantum-physical Model System

Computer-assisted methods aid Heidelberg physicists in reproducing experiment with ultracold atoms

Two researchers at Heidelberg University have developed a model system that enables a better understanding of the processes in a quantum-physical experiment...

Im Focus: Glacier bacteria’s contribution to carbon cycling

Glaciers might seem rather inhospitable environments. However, they are home to a diverse and vibrant microbial community. It’s becoming increasingly clear that they play a bigger role in the carbon cycle than previously thought.

A new study, now published in the journal Nature Geoscience, shows how microbial communities in melting glaciers contribute to the Earth’s carbon cycle, a...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Expert meeting “Health Business Connect” will connect international medical technology companies

20.04.2017 | Event News

Wenn der Computer das Gehirn austrickst

18.04.2017 | Event News

7th International Conference on Crystalline Silicon Photovoltaics in Freiburg on April 3-5, 2017

03.04.2017 | Event News

 
Latest News

New quantum liquid crystals may play role in future of computers

21.04.2017 | Physics and Astronomy

A promising target for kidney fibrosis

21.04.2017 | Health and Medicine

Light rays from a supernova bent by the curvature of space-time around a galaxy

21.04.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>