Researchers at Cornell University have developed a powerful new genetic tool that allows scientists to study how genes work at the level of individual cells, an advance that could accelerate discoveries in development, neuroscience and disease.
The system is based on MAGIC (Mosaic Analysis by gRNA-Induced Crossing-over), a method pioneered by the laboratories of Chun Han, assistant professor in the Department of Molecular and Genetic Biology in the College of Agriculture and Life Sciences (CALS) and the Weill Center for Cell and Molecular Biology. MAGIC uses CRISPR gene editing to produce individual mutant cells within other normal cells, resulting in an exact replication within the organism.
In a new study, get a degree researcher Yifan Shen expanded this method into a genome-wide tool for Drosophila melanogastercreating tools that work on whole chromosomes and allow researchers to study genes that were previously difficult, or impossible, to analyze at single-cell resolution.
“It saves at least a few months for studying one change compared to traditional methods,” Han said. “If one wants to watch hundreds or thousands of changes, the time saved will be years or more.”
Traditional mosaic testing often requires researchers to spend weeks or months piecing together pieces of the gene before testing can begin. On the other hand, the extended MAGIC system works directly with existing genes, greatly reducing technical restrictions while relying on standard laboratory equipment.
The kit also produces enhanced fluorescent markers that make transformed cells brighter and easier to follow under a microscope. In earlier versions, seeing good cell shapes can be difficult.
“Our final design illuminated all the neurons beautifully, right down to the finest branches,” Han said. “This has been a great help for analyzing the dendrite morphology of neurons.”
With genome-wide coverage, the system opens the door to large-scale genetic screens at single-cell resolution. Researchers can now combine MAGIC with existing tools such as Drosophila deficiency libraries to systematically scan the genome for genes involved in important biological processes.
“Many basic biological processes are still poorly understood due to the inability to analyze all genes at the individual cell level,” Han said. “The combination of sparse libraries and MAGIC tools greatly accelerates the process of gene discovery.”
The researchers also demonstrated that the system works on hybrids from different Drosophila species, applications that were difficult or impossible with previous tools.
“This method should allow researchers to ask some very interesting questions about diversity in ways that have not been possible before,” Han said.
Additionally, the team overcame long-standing technical challenges related to the fly’s fourth chromosome, a region that was difficult to study. A new suite of tools enables more reliable analysis of genes on that chromosome, which can reveal biological functions that were previously overlooked.
To increase accessibility, the researchers made the toolkit widely available through public repositories, allowing other labs to adopt the system without special training.
“We have benefited greatly from the supportive Drosophila community,” Han said. “If other laboratories can now use our system to study their important questions in a way that was not possible before, we feel that we have achieved our goals.”
In 2021, Han’s laboratory, along with the laboratory of Mariana Wolfner, Distinguished Professor of Molecular Biology and Genetics and Stephen H. Weiss Presidential Fellow of CALS, began developing the MAGIC instrument. The new study was funded by the National Institutes of Health, and the Weill Center for Cell and Molecular Biology. All of the documents produced in this investigation are housed in Bloomington Drosophila Stock Center, and molecular resources are available through Addgene, ensuring broad access for the research community.
Henry C. Smith is a consultant for Biological Systems Cornell Research and Innovation.
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