CRISPR-Cas9 is a genome editing system. CRISPR systems provides immunity to bacteria and archaea from viruses and has been adapted for use as a genome editing tool capable of knocking out genes and rewriting genetic sequences in animal, plant and fungi. CRISPR-Cas9 is being adapted to other applications outside genome editing.

CRISPR-Cas9 is a genome editing system. The system originates in bacteria providing immunity to viruses and has been adapted for use as a genome editing tool capable of knocking out genes and rewriting genetic sequences in animal, plant and fungi. Outside of genome editing, modifications to the CRISPR-Cas9 system make it useful for gene regulation, genome imaging and studying protein-genome interactions.


Cas9 is the nuclease enzyme that does the cutting in the Type II CRISPR systems used by Streptococcus thermophilis . The function of Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) sequences that are part of a bacterial immune system, was discovered in the yogurt bacteria Streptococcus thermophilus . Phillipe Horvath and Rodolphe Barrangou of Danisco (later DuPont) made that discovery and in 2007 reported in Science that the bacteria incorporate sequences from phage viruses they have been exposed to as spacers in the CRISPR region which gave the bacteria resistance to those phage viruses . DuPont has patented a technique of exposing bacteria to different phage viruses and uses CRISPR sequences to tell them which ones have acquired resistance, something that helps them avoid phage viruses spoiling their yogurt .

Horvath and Barrangou teamed up with Virginjus Siksnys at Vilnius University, Lithuania and they published how CRISPR works with Cas9 in 2012 . Around the same time UC Berkeley’s Jennifer Doudna and Emmanuelle Charpentier now at the Max Planck Institute for Infection Biology, Berlin also described in Science how Cas9 works in the CRISPR system . Because they also engineered a simpler version of CRISPR that could likely to work in other organisms including human cells , this transformed this bacterial immune function into a usable biotechnology tool.

There is a patent dispute over the invention of CRISPR-Cas9 technology specifically for use in human cells, between Doudna’s research team and Feng Zhang’s group at the Broad Institute (MIT and Harvard) . Zhang’s research group and George Church’s lab at Harvard Medical School, each published Science papers in 2013 showing they had modified CRISPR-Cas9 to edit the genome in human and mouse cells . The Broad Institute’s US patent, the first of several for mammalian use of CRISPR, is under appeal . Citing lack of novelty, the European patent office has revoked the first patent obtained by the Broad Institute and has granted patents to the University of California and University of Vienna . The first is for using the CRISPR-Cas9 system across prokaryotic and eukaryotic systems and the second is for a modified form of CRISPR-Cas9 to regulate gene expression.

Genome Editing

Targeting of Cas9 to cleave DNA in bacterial immune function uses two RNAs which form a duplex, the crRNA that recognizes the invading DNA and the tracrRNA which hybridizes with the crRNA . Doudna’s group engineered the system to use a single guide RNA . The CRISPR-Cas9 genome engineering system uses a single protein, Cas9, and single guide-RNA complex (Cas9-sgRNA) and it is the most commonly used CRISPR system for gene editing . The CRISPR-Cas9 user designed guide RNA binds DNA that contains the complementary sequence. The presence of a nearby (protospacer-adjacent motif) PAM sequence is required for cleavage in the target region. For endogenous CRISPR systems in bacteria, absence of PAM sequences in the bacteria’s own genome prevent self cleavage . In the human genome, the short PAM sequence is present at a frequency of 5.21% .

After CRISPR-Cas9 cleaves the DNA, the double stranded break triggers repair by either non-homologous end joining (NHEJ) or homology-directed repair (HDR) . NHEJ can knockout gene function due to random insertions or deletions occur at the site that disrupt the reading frame or change the protein coded for by the sequence. Researchers take advantage of the HDR mechanism by supplying a user-generated DNA template which is used to correct the break. In this way a gene mutation can be cut out and replaced with a corrected version of the gene. Scientists use CRISPR-Cas9 to alter genes in model organisms and cell lines to learn the function of those genes. CRISPR-Cas9 is also being used to develop therapies to treat or cure genetic diseases.

A modified form of CRISPR-Cas9 where dCas9 cannot cut DNA but maintains the ability to target DNA. When fused with transcriptional activators and repressors it can turn gene expression up or down. Similarly, Epigenomic CRISPR-Cas9 systems are fused to proteins that recruit epigenetic modifiers to a target genomic region, resulting in changes in gene expression.


There are clinical trials at Hangzhou Cancer Hospital, China and in the US by University of Pennsylvania researchers where the human immune cells, T-cells are removed from patients, modified by CRISPR-Cas9 in a way that enhances their ability to fight cancer, and put back into the patients .

Blood Disorders

In collaboration CRISPR Therapeutics and Vertex Pharmaceuticals are using CRISPR-Cas9 outside the body to correct a genetic mutation in blood cells of patients with Beta-Thalassemia and Sickle Cell Disease . Clinical trials for these diseases using CRISPR have been put on hold in the US to resolve questions about safety .


Editas Medicine is developing a CRISPR-Cas9 therapy for Leber Hereditary Amaurosis . Autosomal recessive and autosomal dominant Retinitis Pigmentosa, choroidal neovascularization and Age-Related Macular Degeneration are forms of blindness that are being tested with CRISPR-Cas9 preclinically in animal models .

Cystic Fibrosis

CRISPR can fix the Cystic Fibrosis (CF) mutation in lung cells, intestinal cells, and iPS cells derived from patients . Editas Medicine and CRISPR Therapeutics are working towards a therapy to use on CF patients .

Duchenne Muscular Dystrophy

Research in mice demonstrates CRISPR-Cas9 can fix Duchenne Muscular Dystropy (DMD) mutations . However since there are many mutations that cause the disease in humans and one in three are new mutations, it is a challenge to design a gene editing fix that works for more than just one mutation . Eric Olsen and his team at University of Texas Southwestern Medical Center developed a CRISPR-Cas9 gene editing technique that targets 3000 types of DMD mutations . Their system uses 12 guide RNAs that target mutation hotspots to restore heart muscle function in human heart tissue derived from patients . Their system causes changes splice sites so that most commonly mutated sections of the RNA coding for the protein are skipped, a strategy called exon-skipping or myoediting. The resulting protein while still incomplete is still able to function well enough.


February 13, 2013

Zhang and Church each publish papers with CRISPR-Cas9 editing in human cells

August 17, 2012

Doudna and Charpentier describe how CRISPR works and engineer simpler form of CRISPR-Cas9

March 23, 2007

Barrangou and Horvath publish that bacteria use CRISPR to aquire resistance to viruses



Emmanuelle Charpentier

Eric Olsen

Feng Zhang

George Church

Jennifer Doudna

Philippe Horvath

Rodolphe Barrangou

Virginjus Siksnys

Further reading


A CRISPR-Cas9 System for Genetic Engineering of Filamentous Fungi

Christina S. Nødvig, Jakob B. Nielsen, Martin E. Kogle, Uffe H. Mortensen


A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans

Rebecca S Shapiro, Alejandro Chavez, Caroline B M Porter, Meagan Hamblin, Christian S Kaas, James E Dicarlo, Guisheng Zeng, Xiaoli Xu, Alexey V Revtovich, Natalia V Kirienko, Yue Wang, George M Church, James J Collins


CRISPR/Cas9 in Genome Editing and Beyond

Wang, H., La Russa, M. and Qi, L.S.

Safeguarding CRISPR-Cas9 gene drives in yeast

James E Dicarlo, Alejandro Chavez, Sven L Dietz, Kevin M Esvelt, George M Church


Xconomy: Pre-Existing Immunity to CRISPR Found in 96% of People in Study


Documentaries, videos and podcasts


TED - How CRISPR let's us edit our DNA | Jennifer Doudna




Caribou Biosciences

CRISPR Therapeutics

Editas Medicine

ERS Genomics

Intellia Therapeutics

Vertex Pharmaceuticals


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