Scientists have successfully developed a far easier way to manipulate different genes by using a common research model, baker’s yeast.

CRISPR has before helped refine and accelerate the process of gene manipulation, but using the new technique investigators are now able to pick certain cells out of a group when they had specific features, and could then later find the changes that occurred genetically to cause the change. The results of this study have been published in Nature Biotechnology

“Our method not only offers a more efficient and precise way to perform high-throughput functional genomics,” in yeast than what was possible with previous methods. It will also allow us to model and test subtle human gene variations in yeast cells that have been loosely associated with certain traits or disorders, and find out which ones may actually be relevant” said George Church, who is Professor of Genetics at Harvard Medical School (HMS) and of Health Sciences and Technology at Harvard and the Massachusetts Institute of Technology (MIT). 

Using the gene-editing tool CRISPR, the scientists were able to focus on a specific part of the genome, guided by a small piece of RNA called sgRNA that is made by an investigator. The gene editor makes a cut where the sgRNA targets and cellular machinery comes in to make a repair. That process can be aided with a template added by a researcher, so that the cell’s repair mechanism, hormology-directed recombination (HDR), will change the genome in a specific place and in a specific way to reflect the desired edit. 

“We have developed a strategy that physically links the blueprints for sgRNA and donor template in one stable and heritable extra-chromosomal DNA molecule. This enabled us to construct large libraries of variants in one reaction, deliver multiple corresponding srRNAs and donor templates en masse to yeast cells, and identify those that stimulate a certain cell behavior by next-generation sequencing,” added postdoctoral fellow and a first author Xiaoge Guo. 

During this work, the researchers demonstrated that their technique works by changing the gene of a critical enzyme in a large number of yeast cells. The surviving cells in the yeast population were then subjected to sequencing. This revealed the mutations that had allowed for their survival. The team also edited out members of a yeast gene family which little is known about. This enabled them to assign potential functions to the genes after subjecting the edited yeast to varying environmental conditions.

“Besides using the method to tease new functions out of genes and larger families, an intriguing potential also lies in the investigation of non-coding sequences in the genome to advance our understanding of gene regulation and chromosome biology,” commented first and co-corresponding author Alejandro Chavez, an Assistant Professor at Columbia University who was mentored by Church. 

“We can also use the guide and donor method for synthetic biology applications that aim to engineer yeast cells with specific metabolic and industrially relevant abilities, or transfer it to pathological yeast strains for the discovery of genes and gene functions that affect their infectious properties,” noted James Collins, a Professor of Biological Engineering at MIT who part of the study.

“The newest application of the CRISPR-Cas9 technology that emerged through a dynamic collaboration between the Church and Collins labs opens yet another path towards discovery of previously hidden molecular mechanisms by which cells regulate their physiology, and when dysregulated, lead to infectious as well as human disease,” concluded Wyss Founding Director, Donald Ingber, who also holds appointments at HMS, Boston Children’s Hospital, and is Professor of Bioengineering at the Harvard John A. Paulson School of Engineering and Applied Sciences.