While the CRISPR/Cas9 genome editing system has been “burning up the charts”, so to speak, with its extraordinary versatility and potential for treating a host of diseases, until now its editing capabilities have been limited to DNA. Whereas DNA editing makes permanent changes to the genome of a cell, a CRISPR-based RNA-targeting approach would allow investigators to make temporary changes that can be tuned up or down, and with greater specificity and functionality than existing methods for RNA interference.
Now, researchers from the Broad Institute of MIT and Harvard—led by Feng Zhang, Ph.D., who aided in the initial developments CRISPR/Cas9—Massachusetts Institute of Technology, the National Institutes of Health, Rutgers University-New Brunswick, and the Skolkovo Institute of Science and Technology have published data that characterizes a new CRISPR system that targets RNA, rather than DNA—opening up a powerful avenue in cellular manipulation.
The research team was able to identify and functionally characterize C2c2, an RNA-guided enzyme capable of targeting and degrading RNA. Their findings revealed that C2c2—the first naturally occurring CRISPR system that targets only RNA to have been identified and initially discovered by this collaborative group in October 2015—helps protect bacteria against viral infection. The scientists were able to demonstrate that C2c2 can be programmed to cleave particular RNA sequences in bacterial cells, making it a valuable addition to the molecular biology toolbox.
“C2c2 opens the door to an entirely new frontier of powerful CRISPR tools,” explained co-senior study author Feng Zhang, Ph.D., a Core Institute Member of the Broad Institute. “There are an immense number of possibilities for C2c2, and we are excited to develop it into a platform for life science research and medicine.”
The RNA-focused action of C2c2 complements the CRISPR/Cas9 system, which targets DNA, the genomic blueprint for cellular identity and function. The capacity to target only RNA, which helps carry out the genomic instructions, offers the ability to manipulate RNA precisely in a high-throughput manner—and manipulate gene function more broadly.
The findings from this study were published recently in Science in an article entitled “C2c2 Is a Single-Component Programmable RNA-Guided RNA-Targeting CRISPR Effector.”
“The study of C2c2 uncovers a fundamentally novel biological mechanism that bacteria seem to use in their defense against viruses,” noted co-senior author Eugene Koonin, Ph.D., senior investigator and leader of the Evolutionary Genomics Group at the NIH. “Applications of this strategy could be quite striking.”
Currently, the most common technique for performing gene knockdown is small interfering RNA (siRNA). According to the research team, C2c2 RNA-editing methods suggest greater specificity and hold the potential for a wider range of applications. For example, adding modules to specific RNA sequences to alter their function—i.e., how they are translated into proteins—would make them valuable tools for large-scale screens and constructing synthetic regulatory networks. Moreover, researchers could harness C2c2 to tag RNAs fluorescently as a means to study their trafficking and subcellular localization.
In the current study, the team was able to target precisely and remove specific RNA sequences using C2c2—lowering the expression level of the corresponding protein. This suggests C2c2 could represent an alternate approach to siRNA, complementing the specificity and simplicity of CRISPR-based DNA editing and offering researchers an adjustable gene “knockdown” capability using RNA.
C2c2 has some key advantages going for it that should easily enable it to be developed into a major molecular tool: C2c2 is a two-component system, requiring only a single guide RNA to function, and it is genetically encodable—meaning the necessary components can be synthesized as DNA for delivery into tissue and cells.
“C2c2's greatest impact may be made on our understanding the role of RNA in disease and cellular function,” remarked co-first author Omar Abudayyeh, a graduate student in Dr. Zhang’s laboratory.
