Satellite Banner
Genomics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

Speeding up Gene Discovery

Published: Friday, December 13, 2013
Last Updated: Friday, December 13, 2013
Bookmark and Share
New gene-editing system enables large-scale studies of gene function.

Since the completion of the Human Genome Project, which identified nearly 20,000 protein-coding genes, scientists have been trying to decipher the roles of those genes. A new approach developed at MIT, the Broad Institute, and the Whitehead Institute should speed up the process by allowing researchers to study the entire genome at once.

The new system, known as CRISPR, allows researchers to permanently and selectively delete genes from a cell’s DNA. In two new papers, the researchers showed that they could study all the genes in the genome by deleting a different gene in each of a huge population of cells, then observing which cells proliferated under different conditions.

“With this work, it is now possible to conduct systematic genetic screens in mammalian cells. This will greatly aid efforts to understand the function of both protein-coding genes as well as noncoding genetic elements,” says David Sabatini, a member of the Whitehead Institute, MIT professor of biology, and a senior author of one of the papers, both of which appear in this week’s online edition of Science.

Using this approach, the researchers were able to identify genes that allow melanoma cells to proliferate, as well as genes that confer resistance to certain chemotherapy drugs. Such studies could help scientists develop targeted cancer treatments by revealing the genes that cancer cells depend on to survive.

Feng Zhang, the W.M. Keck Assistant Professor in Biomedical Engineering and senior author of the other Science paper, developed the CRISPR system by exploiting a naturally occurring bacterial protein that recognizes and snips viral DNA. This protein, known as Cas9, is recruited by short RNA molecules called guides, which bind to the DNA to be cut. This DNA-editing complex offers very precise control over which genes are disrupted, by simply changing the sequence of the RNA guide.

“One of the things we’ve realized is that you can easily reprogram these enzymes with a short nucleic-acid chain. This paper takes advantage of that and shows that you can scale that to large numbers and really sample across the whole genome,” says Zhang, who is also a member of MIT’s McGovern Institute for Brain Research and the Broad Institute.

Genome-wide screens

For their new paper, Zhang and colleagues created a library of about 65,000 guide RNA strands that target nearly every known gene. They delivered genes for these guides, along with genes for the CRISPR machinery, to human cells. Each cell took up one of the guides, and the gene targeted by that guide was deleted. If the gene lost was necessary for survival, the cell died.

“This is the first work that really introduces so many mutations in a controlled fashion, which really opens a lot of possibilities in functional genomics,” says Ophir Shalem, a Broad Institute postdoc and one of the lead authors of the Zhang paper, along with Broad Institute postdoc Neville Sanjana.

This approach enabled the researchers to identify genes essential to the survival of two populations of cells: cancer cells and pluripotent stem cells. The researchers also identified genes necessary for melanoma cells to survive treatment with the chemotherapy drug vemurafenib.

In the other paper, led by Sabatini and Eric Lander, the director of the Broad Institute and an MIT professor of biology, the research team targeted a smaller set of about 7,000 genes, but they designed more RNA guide sequences for each gene. The researchers expected that each sequence would block its target gene equally well, but they found that cells with different guides for the same gene had varying survival rates.

“That suggested that there were intrinsic differences between guide RNA sequences that led to differences in their efficiency at cleaving the genomic DNA,” says Tim Wang, an MIT graduate student in biology and lead author of the paper.

From that data, the researchers deduced some rules that appear to govern the efficiency of the CRISPR-Cas9 system. They then used those rules to create an algorithm that can predict the most successful sequences to target a given gene.

“These papers together demonstrate the extraordinary power and versatility of the CRISPR-Cas9 system as a tool for genomewide discovery of the mechanisms underlying mammalian biology,” Lander says. “And we are just at the beginning: We’re still uncovering the capabilities of this system and its many applications.”

Efficient alternative

The researchers say that the CRISPR approach could offer a more efficient and reliable alternative to RNA interference (RNAi), which is currently the most widely used method for studying gene functions. RNAi works by delivering short RNA strands known as shRNA that destroy messenger RNA (mRNA), which carries DNA’s instructions to the rest of the cell.

The drawback to RNAi is that it targets mRNA and not DNA, so it is impossible to get 100 percent elimination of the gene. “CRISPR can completely deplete a given protein in a cell, whereas shRNA will reduce the levels but it will never reach complete depletion,” Zhang says.

Michael Elowitz, a professor of biology, bioengineering, and applied physics at the California Institute of Technology, says the demonstration of the new technique is “an astonishing achievement.”

“Being able to do things on this enormous scale, at high accuracy, is going to revolutionize biology, because for the first time we can start to contemplate the kinds of comprehensive and complex genetic manipulations of cells that are necessary to really understand how complex genetic circuits work,” says Elowitz, who was not involved in the research.

In future studies, the researchers plan to conduct genomewide screens of cells that have become cancerous through the loss of tumor suppressor genes such as BRCA1. If scientists can discover which genes are necessary for those cells to thrive, they may be able to develop drugs that are highly cancer-specific, Wang says.

This strategy could also be used to help find drugs that counterattack tumor cells that have developed resistance to existing chemotherapy drugs, by identifying genes that those cells rely on for survival.

The researchers also hope to use the CRISPR system to study the function of the vast majority of the genome that does not code for proteins. “Only 2 percent of the genome is coding. That’s what these two studies have focused on, that 2 percent, but really there’s that other 98 percent which for a long time has been like dark matter,” Sanjana says.

The research from the Lander/Sabatini group was funded by the National Institutes of Health; the National Human Genome Research Institute; the Broad Institute, and the National Science Foundation. The research from the Zhang group was supported by the NIH Director’s Pioneer Award; the NIH; the Keck, McKnight, Merkin, Vallee, Damon Runyon, Searle Scholars, Klingenstein, and Simon Foundations; Bob Metcalfe; the Klarman Family Foundation; the Simons Center for the Social Brain at MIT; and Jane Pauley.


Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 4,000+ scientific posters on ePosters
  • More than 5,300+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Predicting Cancer Cells’ Response to Chemotherapy
Researcher develop method for testing cell ability to perform different types of DNA repair, which can reveal tumors’ sensitivity to drugs.
Wednesday, November 02, 2016
Fighting Cancer with the Power of Immunity
Researchers at MIT have used a combination of four different therapies to activate both of the immune system’s two branches, producing a coordinated attack that led to the complete disappearance of large, aggressive tumors in mice.
Friday, October 28, 2016
Fighting Cancer with Immune Response
New treatment elicits two-pronged immune response that destroys tumors in mice.
Tuesday, October 25, 2016
Linking RNA Structure and Function
Biologists have deciphered a lncRNA structure and used the information to investigate its cellular protein interactions.
Friday, September 09, 2016
Protecting Privacy in Genomic Databases
System helps ensure databases used in medical research will not leak patients’ personal information.
Wednesday, August 10, 2016
Triple-Action Therapy Patch Shows Promise
Patch that delivers drug, gene, and light-based therapy to tumor sites shows promising results in mice.
Wednesday, July 27, 2016
New Device can Study Electric Field Cancer Therapy
Microfluidic device allows study of electric field cancer therapy through low-intensity fields, preventing malignant cells spreading.
Friday, July 08, 2016
Illuminating Hidden Gene Regulators
New super-resolution technique visualizes important role of short-lived enzyme clusters.
Friday, May 27, 2016
A Programming Language for Living Cells
New language lets researchers design novel biological circuits.
Monday, April 04, 2016
Cancer Cells Remodel Environments Before Spreading
Researchers at MIT have found that the cancer cells remodel their environment to make it easier to reach nearby blood vessels.
Wednesday, March 16, 2016
Paving the Way for Metastasis
Cancer cells remodel their environment to make it easier to reach nearby blood vessels.
Tuesday, March 15, 2016
A New Way to Discover DNA Modifications
Researchers systematically find molecules that help regulate and protect DNA.
Wednesday, March 02, 2016
Mapping Regulatory Elements
Systematically searching DNA for regulatory elements indicates limits of previous thinking
Wednesday, February 03, 2016
Curing Disease by Repairing Faulty Genes
New delivery method boosts efficiency of CRISPR genome-editing system.
Wednesday, February 03, 2016
Supply Chain
Chemists discover how a single enzyme maintains a cell’s pool of DNA building blocks.
Wednesday, January 13, 2016
Scientific News
Big Genetics in BC: The American Society for Human Genetics 2016 Meeting
Themes at this year's meeting ranged from the verification, validation, and sharing of data, to the translation of laboratory findings into actionable clinical results.
Personality Traits, Psychiatric Disorders Linked to Specific Genomic Locations
Researchers have unearthed genetic correlations between personality traits and psychiatric disorders.
Genetics Control Regenerative Properties Of Stem Cells
Researchers define how genetic factors control regenerative properties of blood-forming stem cells.
Diabetes Missing Link Discovered
Researchers from the University of Auckland have shown that beta catenin plays a vital role in the control of insulin release from the pancreas.
Study Reveals New Role for Hippo Pathway in Suppressing Cancer Immunity
Hippo pathway signaling regulates organ size by moderating cell growth, apoptosis and stem cell renewal, but dysregulation contributes to cancer development.
Gene-Editing Improves Vision in Blind Rats
Scientists developed a targeted gene-replacement technique that can modify genes in both dividing and non-dividing cells in living animals.
Gene Editing Yields Tomatoes That Ripen Weeks Earlier
Research team develop method to make tomato plants flower and ripen fruit two weeks faster than current growth rates.
Exploring the Genome of the River Blindness Parasite
Researchers have decoded the genome of the parasite that causes the skin and eye infection known as river blindness.
Gene Therapy Maintains Clotting Factor for Hemophilia Patients
Following a single gene therapy dose, the highest levels of an essential blood clotting factor IX were observed in hemophilia B patients.
Unexpected Role for Epigenetic Enzymes in Cancer
Researchers use epigenetics to identify the role of an enzyme family as regulators of genetic message interpretation in yeast.
Skyscraper Banner

SELECTBIO Market Reports
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
4,000+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
5,300+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!