Origin and Development of CRISPR Technology
01
Discovery and Naming
The history of the CRISPR system dates back to early observations of microbial genome structures.
In 1987, Yoshizumi Ishino, a molecular biologist at Osaka University, discovered peculiar repetitive sequences while studying the genome of E. coli
These repeats were 29 bases long and appeared five times, separated by 32-base "spacer" sequences, which appeared unstructured at the time. However, this phenomenon did not attract significant attention back then.
By 2001, the importance of these repetitive sequences began to emerge. Spanish scientist Francisco Mojica discovered through database searches that over 20 species of microbes contained similar repetitive sequences in their genomes.
That same year, Mojica and his colleague Rudd Jansen formally named these clustered, regularly interspaced short palindromic repeats CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats).
02
Mechanism Elucidation and Tool Development
In 2002, Jansen’s team discovered a series of genes accompanying the CRISPR sequences and named them cas genes, which encode Cas proteins. Scientists hypothesized that the CRISPR-Cas system was an immune system used by bacteria to defend against bacteriophage invasion.
Subsequent experiments confirmed this hypothesis: upon viral infection, bacteria carefully excise characteristic sequences of the virus and store them in their own genetic loci (CRISPR arrays). This allows the bacteria to rapidly identify, resist, and evade the virus upon re-infection. This system, composed of CRISPR sequences and Cas proteins, is thus regarded as a form of heritable immune memory.
03
Core Breakthrough
Although the CRISPR mechanism was discovered early on, it was initially considered difficult to manipulate artificially due to the complexity of the natural system, which requires the cooperative action of multiple Cas proteins.
The key breakthrough that propelled the CRISPR-Cas system into the gene-editing revolution occurred in 2012.
In 2012, Emmanuelle Charpentier from Umeå University, Sweden, was the first to discover in in vitro biochemical experiments that a single Cas protein (Cas9, originally termed Csn1) could cleave target DNA when guided by two RNA molecules (crRNA and tracrRNA).
Subsequently, she collaborated with Jennifer Doudna, a structural biologist at the University of California, Berkeley. They engineered the natural dual-RNA system into a single chimeric RNA (sgRNA), significantly simplifying the operation while retaining structural characteristics.
In their seminal paper published in Science in 2012, they demonstrated the potential of the CRISPR-Cas9 system as a gene-editing tool for the first time, confirming that it could function as an RNA-programmed tool to execute targeted cleavage. This system broke through the barriers of previous technologies like ZFNs and TALENs, realizing the scientist’s vision of precise, programmable targeting.
In early 2013, the Cas9 system was applied to artificially designed sequences to achieve high-efficiency gene editing and was successfully implemented in mammalian cells. That same year, Zhang and colleagues developed new methods utilizing the CRISPR-Cas system for targeted genome editing, further improving efficiency and reliability.
04
Continuous Development
In the brief seven years following 2012, CRISPR technology matured rapidly, accompanied by an exponential growth in related publications. Beyond Cas9, CRISPR systems found in an increasing number of bacteria have been excavated and developed into a gene-editing toolbox.
✅ Cas12a (Cpf1): Belonging to the Type V system, its advantage over Cas9 is that it does not require tracrRNA to target and cut DNA. This greatly expands the selection of gene-editing targets and addresses certain limitations of the CRISPR-Cas9 system.
✅ Cas13a: Capable of specifically targeting and cleaving RNA, used for inhibiting endogenous RNA in mammalian cells.
✅ Derivative Tools: Researchers have also utilized the Cas protein scaffold to develop derivative tools that edit without generating double-strand breaks, such as Base Editors and Prime Editing tools. These innovations have introduced new paradigms to gene editing.
The rapid evolution and diversity of CRISPR systems have demonstrated immense potential in fields such as functional genomics, transcriptional regulation, and DNA imaging.
Although the CRISPR-Cas system still faces challenges such as off-target effects, with a deepening understanding of its molecular mechanisms, it is poised to be better applied in human gene therapy, targeted drug discovery, and the creation of animal models for human diseases, benefiting the lives of ordinary people in the near future.
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