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 The balancing act: An enzyme that links endocytosis to membrane recycling
07.12.2016 | National Centre for Biological Sciences

nachricht Transforming plant cells from generalists to specialists
07.12.2016 | Duke University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Significantly more productivity in USP lasers

In recent years, lasers with ultrashort pulses (USP) down to the femtosecond range have become established on an industrial scale. They could advance some applications with the much-lauded “cold ablation” – if that meant they would then achieve more throughput. A new generation of process engineering that will address this issue in particular will be discussed at the “4th UKP Workshop – Ultrafast Laser Technology” in April 2017.

Even back in the 1990s, scientists were comparing materials processing with nanosecond, picosecond and femtosesecond pulses. The result was surprising:...

Im Focus: Shape matters when light meets atom

Mapping the interaction of a single atom with a single photon may inform design of quantum devices

Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

NTU scientists build new ultrasound device using 3-D printing technology

07.12.2016 | Health and Medicine

The balancing act: An enzyme that links endocytosis to membrane recycling

07.12.2016 | Life Sciences

How to turn white fat brown

07.12.2016 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>