CRISPR

Clustered regularly interspaced short palindromic repeats (CRISPR) is a prokaryotic adaptive immune response that provides immunity against foreign nucleic acids, particularly viral DNA or RNA, through the use of crRNAs (CRISPR RNAs) and associated Cas genes.

The CRISPR response evolved to defend bacteria and archaea against infection with bacteriophages, and CRISPR genes are present in the majority of bacterial and archaeal genomes. CRISPR systems share several common features: first, a mechanism for recognition and processing of foreign nucleic acids into short 'spacer' sequences; second, a mechanism for incorporation of these spacers into clusters (CRISPRs) on the bacterial genome, which are regularly interspersed by a short, repeated palindromic DNA sequence; third, a mechanism for transcribing and processing this CRISPR sequence into RNA molecules (known as CRISPR RNAs, or crRNAs) comprising the spacer sequence and a hairpin formed by the palindromic repeat; and finally, recognition and cleavage of DNA or RNA matching the spacer sequence by a protein-RNA complex consisting of both the crRNA and a nuclease. To avoid self-cleavage of the CRISPR locus in the microbe's genome, spacer sequences must occur next to a short DNA sequence, called the Protospacer-Adjacent Motif (PAM), which is not present in the CRISPR locus of the genome. This PAM sequence must be present in order for a spacer to be incorporated into the CRISPR locus, and must be present next to DNA/RNA matching the spacer in order for the crRNA/nuclease complex to recognize and cleave it. The genes and proteins involved with spacer acquisition, crRNA processing, and crRNA-guided cleavage are named CRISPR-Associated (Cas). In type II CRISPR systems, a single gene called Cas9 produces a DNA endonuclease which binds to the crRNA (which, when fused with a trans-activating crRNA, is called a short guide RNA or sgRNA), and can bind and introduce DNA double strand breaks at sequences matching the crRNA's spacer region. The Cas9/sgRNA complex can be programmed to cleave any PAM-adjacent DNA sequence, simply by changing the the spacer (also known as the guide) sequence. Cas nucleases from type V CRISPR systems (such as Cpf1/Cas12A) have also been adapted to programmably cleave DNA, while nucleases from type VI CRISPR systems (such as C2c2/Cas13A) have been adapted to programmably cleave RNA.

CRISPR has been rapidly adopted in biotechnology research as it offers rapid genetic editing at a fraction of the time and cost of previous approaches. Whereas previous gene-editing approaches required protein engineering for each edit, CRISPR can be re-directed to a new site in the genome through supply of a new sgRNA/crRNA complementary to the site of interest. While the first CRISPR variants based around native Cas9 suffered from high off-target mutagenesis rates, protein engineering and the discovery of additional CRISPR variations in bacterial species has led to a rapid proliferation of Cas9-related endonucleases, each with their own benefits and trade-offs. This family of tools is generally referred to as CRISPR. It comprises CRISPRa/CRISPRi acting as artificial transcription factors to regulate gene expression, high-fidelity CRISPR editing tools, drug-inducible endonucleases, molecular imaging tools for DNA binding interactions, and highly sensitive and specific detectors of both DNA and RNA. CRISPR systems are undergoing rapid development worldwide with application to diverse areas such as therapeutics, research tools, and ecological engineering. These developments have highlighted the potential safety issues inherent in a powerful genome editing technology.