Summary: CRISPR associated protein
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "CRISPR". More...
The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.
Does Pfam agree with the content of the Wikipedia entry ?
Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.
Editing Wikipedia articles
Before you edit for the first time
Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.
You should take a few minutes to view the following pages:
How your contribution will be recorded
Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.
If you have problems editing a particular page, contact us at firstname.lastname@example.org and we will try to help.
The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.
CRISPR Edit Wikipedia article
Clustered regularly interspaced short palindromic repeats (CRISPR, pronounced crisper) are segments of prokaryotic DNA containing short repetitions of base sequences. Each repetition is followed by short segments of "spacer DNA" from previous exposures to a bacteriophage virus or plasmid.
The CRISPR/Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages, and provides a form of acquired immunity. CRISPR spacers recognize and cut these exogenous genetic elements in a manner analogous to RNA interference in eukaryotic organisms. CRISPRs are found in approximately 40% of sequenced bacterial genomes and 90% of sequenced archaea.[note 1]
The CRISPR interference technique has enormous potential application, including altering the germline of humans, animals, and other organisms and modifying the genes of food crops. By delivering the Cas9 protein and appropriate guide RNAs into a cell, the organism's genome can be cut at any desired location. CRISPRs have been used in concert with specific endonuclease enzymes for genome editing and gene regulation in species throughout the tree of life. Ethical concerns have been expressed about the prospect of using this nascent biotechnology for editing the human germline.
- 1 History
- 2 Locus structure
- 3 Mechanism
- 4 Evolution and diversity
- 5 Identification
- 6 Evolutionary significance
- 7 Use by phages
- 8 Applications
- 9 Patents and commercialization
- 10 Society and culture
- 11 See also
- 12 Notes
- 13 References
- 14 Further reading
CRISPR is part of a normally occurring bacterial process. Bacteria may incorporate foreign DNA and even scavenge damaged DNA from their environment.
Clustered repeats were first described in 1987 for the bacterium Escherichia coli by Osaka University researcher Yoshizumi Ishino, but at that time their function was not known. The repeats were observed independently by Spanish researcher Francisco Mojica in 1993. He would later name them short regularly spaced repeats (SRSR) after he found them in many other microbes. In 2000, similar repeats were identified in other bacteria and archaea. SRSR was renamed CRISPR in 2002 after a suggestion from Mojica. CRISPR was proposed as being responsible for the generation of adaptive immunity in microbes. The paper describing this idea was initially rejected by a number of high-profile journals. Papers proposing similar hypotheses by Gilles Vergnaud and, independently, Alexander Bolotin suffered similar fates before ultimately being published.  
A set of genes was found to be associated with CRISPR repeats and was named the cas, or CRISPR-associated genes. The cas genes encode putative nuclease or helicase proteins, which are enzymes that can cut or unwind DNA, respectively.
In 2005, three independent research groups showed that some CRISPR spacers are derived from phage DNA and extrachromosomal DNA such as plasmids.  In effect, the spacers are fragments of DNA gathered from viruses that have previously tried to attack the cell. The source of the spacers was a sign that the CRISPR/cas system could have a role in adaptive immunity in bacteria. Koonin and colleagues proposed that spacers serve as a template for RNA molecules, analogous to a system called RNA interference used by eukaryotic cells.
In 2007, Barrangou, Horvath (food industry scientists at Danisco), and Moineau's group at Université Laval (Canada) showed that they could use spacer DNA to alter the resistance of Streptococcus thermopiles to phage attack.
Feng Zhang and colleagues first described genome editing in human and mouse cell culture using CRISPR/Cas Systems. It has since been used in a wide range of organisms, including baker's yeast, (Saccharomyces cerevisiae), zebrafish, (D. rerio), fruit flies (Drosophila melanogaster), axolotl, (A. mexicanum), nematodes, (C. elegans), plants, mice, monkeys, and human embryos.
In 2012, Jennifer Doudna and Emmanuelle Charpentier first showed CRISPR to work as a genome-engineering and editing tool in bacterial cell cultures.[better source needed] The team had independently been exploring CRISPR-associated proteins to learn how bacteria use spacers in their immune defenses.[better source needed] They jointly studied a simpler CRISPR system that relies on a protein called Cas9. They found that bacteria respond to an invading phage by transcribing spacers and palindromic DNA into a long RNA molecule. The cell then uses tracrRNA and Cas9 to cut this long RNA molecule into pieces called crRNAs.
Cas9 is a nuclease, an enzyme specialized for cutting DNA. It has two active cutting sites (HNH and RuvC), one for each strand of the DNA's double helix. Doudna and Charpentier demonstrated that they could disable one or both sites while preserving Cas9's ability to home in on its target DNA. In 2012, a group including both Doudna and Charpentier combined tracrRNA and spacer RNA into a "single-guide RNA" molecule that, mixed with Cas9, could find and cut the correct DNA targets. Their study proposed that such synthetic guide RNAs could be used for gene editing.
In the early 2000s, researchers developed zinc finger nucleases, synthetic proteins whose DNA-binding domains enable them to create double-stranded breaks in DNA at specific points. In 2010, synthetic nucleases called TALENs provided an easier way to target a double-stranded break to a specific location on the DNA strand. Both zinc finger nucleases and TALENs require the creation of a custom protein for each targeted DNA sequence, which is a more difficult and time-consuming process than that for guide RNAs. CRISPRs are much easier to design because the process requires only making a short RNA sequence.
Repeats and spacers
CRISPR repeats range in size from 24 to 48 base pairs. They usually show some dyad symmetry, implying the formation of a secondary structure such as a hairpin, but are not truly palindromic. Repeats are separated by spacers of similar length. Some CRISPR spacer sequences exactly match sequences from plasmids and phages,   although some spacers match the prokaryote's genome (self-targeting spacers).  New spacers can be added rapidly as part of the immune response to phage infection.
Cas genes and CRISPR subtypes
cas genes are often associated with CRISPR repeat-spacer arrays. Comparative genomics identified multiple cas genes; an initial analysis of 200 bacterial and archaeal genomes suggested as many as 45 cas gene families. Only ''cas1'' and cas2 genes are present in all 45 families.
The current CRISPR classification groups cas operons into three major divisions: I, II, and III, each with multiple subdivisions based on ''cas1'' phylogeny and cas operon gene complement. Aside from cas1 and cas2, each major division's operons have a common set of constituent genes. Each subdivision is characterised by a ‘signature gene’ found exclusively in that subdivision. Many organisms contain multiple CRISPR-Cas systems suggesting that they are compatible and may share components. The sporadic distribution of the CRISPR/Cas subtypes suggests that the CRISPR/Cas system is subject to horizontal gene transfer during microbial evolution.
|Cas type||Signature gene||Function||Reference|
|I||Cas3||Single-stranded DNA nuclease (HD domain) and ATP-dependent helicase|||
|IA||Cas8a||Subunit of the interference module. Important in targeting of invading DNA by recognizing the PAM sequence|||
|ID||Cas10d||contains a domain homologous to the palm domain of nucleic acid polymerases and nucleotide cyclases|||
|II||Cas9||Nucleases RuvC and HNH together produce DSBs, and separately can produce single-strand breaks. Ensures the acquisition of functional spacers during adaptation.|||
|IIA||Csn2||Ring-shaped DNA-binding protein. Involved in primed adaptation in Type II CRISPR system.|||
|IIC||Characterized by the absence of either Csn2 or Cas4|||
|III||Cas10||Homolog of Cas10d and Cse1|||
When a microbe is invaded by a virus, the first stage of the immune response is to capture viral DNA and insert it into a CRISPR locus in the form of a spacer. Cas1 and Cas2 are found in all three types of CRISPR-Cas immune systems, which indicates that they are involved in spacer acquisition. Mutation studies confirmed this hypothesis, showing that removal of cas1 or cas2 stopped spacer acquisition, without affecting CRISPR immune response.
Multiple Cas1 proteins have been characterised and their structures resolved. Cas1 proteins have diverse amino acid sequences. However, their crystal structures are similar and all purified Cas1 proteins are metal-dependent nucleases/integrases that bind to DNA in a sequence-independent manner. Representative Cas2 proteins have been characterised and possess either ssRNA- or dsDNA- specific endoribonuclease activity.
In the I-E system of E. coli Cas1 and Cas2 form a complex where a Cas2 dimer bridges two Cas1 dimers. In this complex Cas2 performs a non-enzymatic scaffolding role, binding double-stranded fragments of invading DNA, while Cas1 binds the single-stranded flanks of the DNA and catalyses their integration into CRISPR arrays.
Protospacer adjacent motifs
Bioinformatic analysis of regions of phage genomes that were excised as spacers (termed protospacers) revealed that they were not randomly selected but instead were found adjacent to short (3 – 5 bp) DNA sequences termed protospacer adjacent motifs (PAM). Analysis of CRISPR-Cas systems from the three major divisions showed PAMs to be important for type I and type II, but not type III systems during acquisition. In type I and type II systems, protospacers are excised at positions adjacent to a PAM sequence, with the other end of the spacer cut using a ruler mechanism, thus maintaining the regularity of the spacer size in the CRISPR array. The conservation of the PAM sequence differs between CRISPR-Cas systems and appears to be evolutionarily linked to Cas1 and the leader sequence.
New spacers are added to a CRISPR array in a directional manner, occurring preferentially, but not exclusively, adjacent to the leader sequence. Analysis of the type I-E system from E. coli demonstrated that the first direct repeat, adjacent to the leader sequence is copied, with the newly acquired spacer inserted between the first and second direct repeats.
The PAM sequence appears to be important during spacer insertion in type I-E systems. That sequence contains a strongly conserved final nucleotide (nt) adjacent to the first nucleotide of the protospacer. This nucleotide becomes the final base in the first direct repeat. This suggests that the spacer acquisition machinery generates single-stranded overhangs in the second-to-last position of the direct repeat and in the PAM during spacer insertion. However, not all CRISPR-Cas systems appear to share this mechanism as PAMs characterised in other organisms do not show the same level of conservation in the final position. It is likely that in those systems, a blunt end is generated at the very end of the direct repeat and the protospacer during acquisition.
Recent analysis of Sulfolobus solfataricus CRISPRs revealed further complexities to the canonical model of spacer insertion as one of its six CRISPR loci inserted new spacers randomly throughout its CRISPR array, as opposed to inserting closest to the leader sequence.
Multiple CRISPRs contain many spacers to the same phage. The mechanism that causes this phenomenon was elucidated in the type I-E system of E. coli. A significant enhancement in spacer acquisition was detected where spacers already target the phage, even mismatches to the protospacer. This ‘priming’ requires the Cas proteins involved in both acquisition and interference to interact with each other. Newly acquired spacers that result from the priming mechanism are always found on the same strand as the spacer that caused the priming. This observation led to the hypothesis that the acquisition machinery slides along the foreign DNA after priming to find a new protospacer.
The CRISPR immune response occurs through two steps: CRISPR-RNA (crRNA) biogenesis and crRNA-guided interference.
The crRNA is initially transcribed as part of a single long transcript encompassing much of the CRISPR array. This transcript is then cleaved by Cas proteins to form crRNAs. The mechanism to produce crRNAs differs among CRISPR-Cas systems. In type I-E and type I-F systems, the proteins Cas6e and Cas6f respectively, recognise stem-loops created by the pairing of identical repeats which flank the crRNA. These Cas proteins cleave the longer transcript at the edge of the paired region, leaving a single crRNA along with a small remnant of the paired repeat region.
Type III systems also use Cas6, however their repeats do not produce stem-loops. Cleavage instead occurs by the longer transcript wrapping around the Cas6 to allow cleavage just upstream of the repeat sequence.
Type II systems lack the Cas6 gene and instead utilize RNaseIII for cleavage. Functional type II systems encode an extra small RNA that is complementary to the repeat sequence, known as a trans-activating RNA (tracrRNA). Transcription of the tracrRNA and the primary CRISPR transcript results in base pairing and the formation of dsRNA at the repeat sequence, which is subsequently targeted by RNaseIII to produce crRNAs. Unlike the other two systems the crRNA does not contain the full spacer but instead is truncated at one end.
CrRNAs associate with Cas proteins to form ribonucleotide complexes that recognize foreign nucleic acids. CrRNAs show no preference between the coding and non-coding strands, which is indicative of an RNA-guided DNA-targeting system. The type I-E complex (commonly referred to as Cascade) requires five Cas proteins bound to a single crRNA.
During the interference stage in type I systems the PAM sequence is recognized on the crRNA-complementary strand and is required along with crRNA annealing. In type I systems correct base pairing between the crRNA and the protospacer signals a conformational change in Cascade that recruits Cas3 for DNA degradation.
Type II systems rely on a single multifunctional protein, Cas9, for the interference step. Cas9 requires both the crRNA and the tracrRNA to function and cleaves DNA using its dual HNH and RuvC/RNaseH-like endonuclease domains. Basepairing between the PAM and the phage genome is also required in type II systems, however the PAM is recognized on the same strand as the crRNA (the opposite strand to type I systems).
Type III systems, like type I require six or seven Cas proteins binding to crRNAs. The type III systems analysed from S. solfataricus and P. furiosus both target the mRNA of phages rather than phage DNA genome, which may make these systems uniquely capable of targeting RNA-based phage genomes.
The mechanism for distinguishing self from foreign DNA during interference is built into the crRNAs and is therefore likely common to all three systems. Throughout the distinctive maturation process of each major type, all crRNAs contain a spacer sequence and some portion of the repeat at one or both ends. It is the partial repeat sequence that prevents the CRISPR-Cas system from targeting the chromosome as base pairing beyond the spacer sequence signals self and prevents DNA cleavage. RNA-guided CRISPR enzymes are classified as type V restriction enzymes.
|CRISPR associated protein|
crystal structure of a crispr-associated protein from thermus thermophilus
|CRISPR associated protein Cas2|
crystal structure of a hypothetical protein tt1823 from thermus thermophilus
Scientists can use viral or non-viral system for delivery of the Cas9 and gRNA into target cells. Electroporation of DNA, RNA or ribonucleocomplexes is the most common and cheapest system. This technique was used to edit CXCR4 and PD-1, knocking in new sequences to replace specific genetic “letters” in these proteins. The group was then able to sort the cells, using cell surface markers, to help identify successfully edited cells. Deep sequencing of a target site confirmed that knock-in genome modifications had occurred with up to ∼20% efficiency, which accounted for up to approximately one-third of total editing events. However, hard-to-transfect cells (stem cells, neurons, hematopoietic cells, etc.) require more efficient delivery systems such as those based on lentivirus (LVs), adenovirus (AdV) and adenoassociated (AAV).
|CRISPR-associated protein Cse1|
|CRISPR-associated protein Cse2|
Evolution and diversity
The basic model of CRISPR evolution is one where newly incorporated spacers drive phages to mutate their genomes to avoid the bacteria immune response, creating diversity in both the phage and host populations. To fight off a phage infection, the sequence of the CRISPR spacer must correspond perfectly to the sequence of the target phage gene. Phages can continue to infect their hosts given point mutations in the spacer. Similar stringency is required in PAM or the bacterial strain will remain phage sensitive.
A study of 124 S. thermophilus strains showed that 26% of all spacers were unique and that different CRISPR loci showed different rates of new spacer acquisition. Particular CRISPR loci evolve more rapidly than others, which allowed the strains' phylogenetic relationships to be determined. A comparative genomic analysis showed that E. coli and S. enterica evolve much more slowly than S. thermophilus. The latter's strains that had diverged 250 thousand years ago still contained the same spacer complement.
Metagenomic analysis of two acid mine drainage biofilms showed that one of the analyzed CRISPRs contained extensive deletions and spacer additions in comparison to the other biofilm, suggesting a higher phage activity/prevalence in one community compared to the other. In the oral cavity, a temporal study determined that 7-22% of spacers were shared over 17 months within an individual while less than 2% of spacers were shared between individuals.
From the same environment a single strain was tracked using PCR primers specific to its CRISPR system. Unlike the broad-level results of spacer presence/absence, which showed significant diversity, this CRISPR added 3 spacers over 17 months, suggesting that even in an environment with significant CRISPR diversity some loci evolve slowly. CRISPRs have also been analysed from the metagenomes produced for the human microbiome project. Although most CRISPRs were body-site specific, some CRISPRs within a body site are widely shared among individuals. One of these CRISPR loci originated from streptococcal species and contained ~15,000 spacers, 50% of which were unique. Similar to the targeted studies of the oral cavity, some of the CRISPRs showed little evolution over time.
CRISPR evolution has been studied in chemostats using S. thermophilus to explicitly examine spacer acquisition rates. In one week, S. thermophilus strains acquired up to three spacers when challenged with a single phage. During the same interval the phage developed single nucleotide polymorphisms that became fixed in the population, suggesting that CRISPR targeting had prevented phage replication absent these mutations. Other S. thermophilus experiments showed that phages can still infect and replicate in hosts that have only one targeting spacer and that sensitive hosts can exist in environments with high phage titres. The chemostat and observational studies suggest many nuances to CRISPR and phage (co)evolution.
CRISPRs are widely distributed among bacteria and archaea and show some sequence similarities. However their most notable characteristic is their repeating spacers and direct repeats. This characteristic makes CRISPRs easily identifiable in long sequences of DNA, since the number of repeat copies decreases the likelihood of a false positive match. Three programs are used for CRISPR repeat identification that search for regularly interspaced repeats in long sequences: CRT, PILER-CR and CRISPRfinder.
Analysis of CRISPRs in metagenomic data is more challenging, as CRISPR loci do not typically assemble due to their repetitive nature or through strain variation, which confuses assembly algorithms. Where many reference genomes are available, polymerase chain reaction (PCR) can be used to amplify CRISPR arrays and analyse spacer content. However, this approach yields information only for specifically targeted CRISPRs and for organisms with sufficient representation in public databases to design reliable PCR primers.
The alternative is to extract and reconstruct CRISPR arrays from shotgun metagenomic data. This is computationally more difficult, particularly with second generation sequencing technologies (e.g. 454, Illumina), as the short read lengths prevent more than two or three repeat units appearing in a single read. CRISPR identification in raw reads has been achieved using purely denovo identification or by using direct repeat sequences in partially assembled CRISPR arrays from contigs (overlapping DNA segments that together represent a consensus region of DNA) and direct repeat sequences from published genomes as a hook for identifying direct repeats in individual reads.
Through the CRISPR/Cas mechanism, bacteria can acquire immunity to certain phages and thus halt further transmission of targeted phages. For this reason, Eugene Koonin has described CRISPR/Cas as a Lamarckian inheritance mechanism. However, this has been disputed by a recent critic noting "We should remember [Lamarck] for the good he contributed to science, not for things that resemble his theory only superficially. Indeed, thinking of CRISPR and other phenomena as Lamarckian only obscures the simple and elegant way evolution really works.
Analysis of CRISPR sequences revealed coevolution of host and viral genomes. Cas9 proteins are highly enriched in pathogenic and commensal bacteria. CRISPR/Cas-mediated gene regulation may contribute to the regulation of endogenous bacterial genes, particularly during interaction with eukaryotic hosts. For example, Francisella novicida uses a unique, small, CRISPR/Cas-associated RNA (scaRNA) to repress an endogenous transcript encoding a bacterial lipoprotein that is critical for F. novicida to dampen host response and promote virulence.
Use by phages
Another way for bacteria to defend against phage infection is by having chromosomal islands. A subtype of chromosomal islands called phage-inducible chromosomal island (PICI) is excised from a bacterial chromosome upon phage infection and can inhibit phage replication. The mechanisms that induce PICI excision and how PICI inhibits phage replication are not well understood. One study showed that lytic ICP1 phage, which specifically targets Vibrio cholerae serogroup O1, has acquired a CRISPR/Cas system that targets a V. cholera PICI-like element. The system has 2 CRISPR loci and 9 Cas genes. It seems to be homologous to the 1-F system found in Yersinia pestis. Moreover, like the bacterial CRISPR/Cas system, ICP1 CRISPR/Cas can acquire new sequences, which allows phage and host to co-evolve.
By the end of 2014 some 600 research papers had been published that mentioned CRISPR. The technology has been used to functionally inactivate genes in human cell lines and cells, to study Candida albicans, to modify yeasts used to make biofuels and to genetically modify crop strains.
CRISPR/Cas9 genome editing is carried out with a Type II CRISPR system. When utilized for genome editing, this system includes Cas9, CRISPR RNA (crRNA), trans-activating crRNA (tracrRNA) along with an optional section of DNA repair template that is utilized in either Non-Homologous End Joining (NHEJ) or Homology Directed Repair (HDR).
|crRNA||Contains the RNA used by Cas9 to guide it to the correct section of host DNA along with a region that binds to tracrRNA (generally in a hairpin loop form) forming an active complex with Cas9|
|tracrRNA||Binds to crRNA and forms an active complex with Cas9|
|sgRNA||Single guide RNAs are a combined RNA consisting of a tracrRNA and at least one crRNA|
|Cas9||Protein that in its active form is able to modify DNA utilizing crRNA as its guide. Many variants exist with differing functions (i.e. single strand nicking, double strand break, DNA binding) due to Cas9's DNA site recognition function that is independent of its two DNA cleaving domains (one for each strand).|
|Repair template||DNA that guides the cellular repair process allowing insertion of a specific DNA sequence|
CRISPR/Cas9 often employs a plasmid to transfect the target cells. The main components of this plasmid are displayed in the image and listed in the table. The crRNA needs to be designed for each application as this is the sequence that Cas9 uses to identify and directly bind to the cell's DNA. The crRNA must bind only where editing is desired. The repair template must also be designed for each application, as it must overlap with the sequences on either side of the cut and code for the insertion sequence.
Multiple crRNA's and the tracrRNA can be packaged together to form a single-guide RNA (sgRNA). This sgRNA can be joined together with the Cas9 gene and made into a plasmid in order to be transfected into cells (see image for overview).
CRISPR/Cas9 is a widely used system for genome editing due to its high degree of fidelity and relatively simple construction. CRISPR/Cas9 depends on two factors for its specificity – the CRISPR target sequence and the PAM. The CRISPR target sequence is 20 bases long as part of each CRISPR locus in the crRNA array. A typical crRNA array has multiple unique target sequences. Cas9 proteins select the correct location on the host's genome by utilizing the sequence for base pair bonding with the host DNA. The sequence is not part of the Cas9 protein and as a result is customizable and can be independently synthesized.
The PAM sequence on the host genome is recognized by the protein structure of Cas9 and generally cannot be easily modified to recognize a difference sequence. However this is not limiting as it is a short sequence and not very specific (e.g. the SpCas9 PAM sequence is 5'-NGG-3' and in the human genome occurs roughly every 8 to 12 base pairs).
Once these have been assembled into a plasmid and transfected into cells the Cas9 protein with help of the crRNA finds the correct sequence in the host cell's DNA and – depending on the Cas9 variant – creates a single or double strand break in the DNA. Properly spaced single strand breaks in the host DNA can trigger homology directed repair, which is less error prone than non-homologous end joining that typically follows a double strand break. Providing a section of DNA repair template allows for the insertion of a specific DNA sequence at an exact location within the genome. The repair template should extend 40 to 90 base pairs beyond the Cas9 induced DNA break. The goal is for the cell's HDR process to utilize the provided repair template and thereby incorporate the new sequence into the genome. Once incorporated, this new sequence is now part of the cell's genetic material and passes into its daughter cells.
Many online tools are available to aid in designing effective sgRNA sequences.
CRISPRs have been used to cut five to 62 genes at once: pig cells have been engineered to inactivate all 62 Porcine Endogenous Retrovirus in the pig genome, which eliminated infection from the pig to human cells in culture. CRISPR's low cost compared to alternatives is widely seen as revolutionary.
- Immunization of industrially important bacteria, including some used in food production and large-scale fermentation
- Cellular or organism RNA-guided genome engineering. Proof of concept studies demonstrated examples both in vitro and in vivo
- Bacterial strain discrimination by comparison of spacer sequences
Like RNAi, CRISPR interference (CRISPRi) turns off genes in a reversible fashion by targeting, but not cutting a site. The targeted site is methylated so the gene is epigenetically modified. This modification inhibits transcription. Cas9 is an effective way of targeting and silencing specific genes at the DNA level. In bacteria, the presence of Cas9 alone is enough to block transcription. For mammalian applications, a section of protein is added. Its guide RNA targets regulatory DNA sequences called promoters that immediately precede the target gene.
Cas9 was used to carry synthetic transcription factors that activated specific human genes. The technique achieved a strong effect by targeting multiple CRISPR constructs to slightly different locations on the gene's promoter.
CRISPR simplifies creation of animals for research that mimic disease or show what happens when a gene is knocked down or mutated. CRISPR may be used at the germline level to create animals where the gene is changed everywhere, or it may be locally targeted.
CRISPR can also be utilized to create human cellular models of disease. For instance, CRISPR was applied to human pluripotent stem cells to introduce targeted mutations in genes relevant to two different kidney diseases, polycystic kidney disease and focal segmental glomerulosclerosis. These CRISPR-modified pluripotent stem cells were subsequently grown into human kidney organoids, which exhibited disease-specific phenotypes. Kidney organoids from stem cells with polycystic kidney disease mutations formed large, translucent cyst structures from kidney tubules. Kidney organoids with mutations in a gene linked to focal segmental glomerulosclerosis developed junctional defects between podocytes, the filtering cells affected in that disease. Importantly, these disease phenotypes were absent in control organoids of identical genetic background, but lacking the CRISPR mutations. A similar approach has been taken to model long QT syndrome in cardiomyocytes derived from pluripotent stem cells. These CRISPR-generated cellular models, with isogenic controls, provide a new way to study human diseases and test drugs that might work in human patients.
In 2003 evolutionary biologist Austin Burt envisioned attaching a gene that coded for a desired trait to “selfish” DNA elements that could copy themselves from one chromosome position to another. That would bias daughter cells to inherit it, quickly spreading it throughout a population. In 2015 a U.S. team used CRISPR to create a “mutagenic chain reaction” that drove a pigmentation trait in lab-grown Drosophila to the next generation with 97% efficiency. With another research group they created a gene drive in mosquitoes that spread genes that prevented the insects from harboring malaria parasites. Only weeks later, the team reported a second drive with genes that rendered female mosquitoes infertile and could quickly wipe out a population. The work was done in the lab, leading to debates over the desirability of field testing.
Using “dead” versions of Cas9 eliminates CRISPR’s DNA-cutting ability, while preserving its ability to target desirable sequences. Multiple groups added various regulatory factors to dead Cas9s, enabling them to turn almost any gene on or off or subtly adjust its level of activity.
Recently, it was demonstrated that CRISPR/Cas-based "RNA-guided nucleases" can be used to target virulence factors, genes encoding antibiotic resistance, and other medically relevant sequences of interest. This technology thus represents a novel form of antimicrobial therapy and a strategy by which to manipulate bacterial populations.
In another 2015 experiment, the 20,000 or so known human genes were separately targeted, turning them on one by one in groups of cells to identify those involved in resistance to a melanoma drug. Each such gene manipulation is itself a separate "drug", potentially opening the entire genome to CRISPR-based regulation.
Clinical researchers are applying it to develop tissue-based treatments for cancer and other diseases.
CRISPR may revive the concept of transplanting animal organs into people. Retroviruses present in animal genomes could harm transplant recipients. In 2015 a team eliminated 62 copies of a retrovirus’s DNA from the pig genome.
It may also have applications in tissue engineering and regenerative medicine, such as by creating human blood vessels that lack expression of MHC class II proteins, which often cause transplant rejection.
In 2015, multiple studies attempted to systematically disable every individual human gene, in an attempt to identify which genes were essential. Between 1,600 and 1,800 genes passed their test—around one in ten. Such genes are more strongly activated, and unlikely to carry disabling mutations. They are more likely to have indispensable counterparts in other species. They build proteins that unite to form larger collaborative complexes. The specific functions of some 18 percent of the essential genes are unidentified. The studies also catalogued the essential genes in four cancer-cell lines and identified genes that are expendable in healthy cells, but crucial in specific tumor types and drugs that could target these rogue genes.
In vitro Genetic Depletion
Unenriched sequencing libraries often have abundant undesired sequences. Cas9 can specifically deplete the undesired sequences with double strand breakage with up to 99% efficiency and without significant off-target effects as seen with restriction enzymes. Treatment with Cas9 has been demonstrated to deplete abundant rRNA while increasing pathogen sensitivity in RNA-seq libraries. 
Patents and commercialization
As of December 2014, patent rights to CRISPR were contested. Several companies had been formed to develop related drugs and research tools. As companies ramp up financing, doubts as to whether or not CRISPR can be successfully monetized in the short-term have been raised.
As of November 2013 SAGE Labs had exclusive rights from one of those companies to produce and sell genetically engineered rats and nonexclusive rights for mouse and rabbit models.
Society and culture
Human germline modification
In light of plans or ongoing research to apply CRISPR to human embryos in at least four labs in the US, labs in China and the UK, and by a US biotechnology company called Ovascience, scientists, including an inventor of CRISPR, urged a worldwide moratorium on applying CRISPR to the human germline, especially for clinical use. They said "scientists should avoid even attempting, in lax jurisdictions, germline genome modification for clinical application in humans" until the full implications "are discussed among scientific and governmental organizations". These scientists support basic research on CRISPR and do not see CRISPR as developed enough for any clinical use in making inheritable changes to people.
In April 2015, scientists from China published a paper in the journal Protein & Cell reporting results of an attempt to alter the DNA of non-viable human embryos using CRISPR to correct a mutation that causes beta thalassemia, a lethal heritable disorder. According to the paper's lead author, the study had previously been rejected by both Nature and Science in part because of ethical concerns; the journals did not comment to reporters. The experiments resulted in changing only some of the genes, and had off-target effects on other genes. The scientists who conducted the research stated that CRISPR is not ready for clinical application in reproductive medicine. One said to a reporter at Nature: "If you want to do it in normal embryos, you need to be close to 100%.... That’s why we stopped. We still think it’s too immature."
In December 2015, the International Summit on Human Gene Editing took place in Washington under the guidance of David Baltimore. Members of national scientific academies of America, Britain and China discussed the ethics of germline modification. In conclusion, they agreed to proceed further with basic and clinical research under appropriate legal and ethical guidelines. A specific distinction was made between clinical use in somatic cells, where the effects of edits are limited to a single individual, versus germline cells, where genome changes would be inherited by future generations. This could have unintended and far-reaching consequences for human evolution, genetically (e.g. gene/environment interactions) and culturally (e.g. Social Darwinism), hence altering of gametocytes and embryos to generate inheritable changes in humans was claimed irresponsible. In addition, they agreed to initiate an international forum where these concerns will be continuously addressed, and regulations in research harmonised across countries.
In February 2016, British scientists were given permission by regulators to genetically modify human embryos by using CRISPR-Cas9 and related techniques. The embryos were to be destroyed after seven days.
American Jennifer Doudna and French-born Emmanuelle Charpentier co-authored a key study published in August 2012 that demonstrated the technical power of Crispr-Cas9 to cut and splice genes with extreme efficiency at the highest resolution possible. In 2012 and 2013, CRISPR was a runner-up in Science Magazine's Breakthrough of the Year award. Sabin Mulepati, a 2014 Johns Hopkins University graduate, was published on the cover of Science Magazine in September 2014. This was for his research on the crystal structure for a CRISPR RNA. In 2015, it was the winner of that award. CRISPR was also named as one of MIT Technology Review's 10 breakthroughs technologies in 2014 and 2016.
- Horvath P, Barrangou R (2010). "CRISPR/Cas, the immune system of bacteria and archaea". Science 327 (5962): 167–70. Bibcode:2010Sci...327..167H. doi:10.1126/Science.1179555. PMID 20056882.
- Sawyer, Eric (9 February 2013). "Editing Genomes with the Bacterial Immune System". Scitable. Nature Publishing Group. Retrieved 6 April 2015.
- Marraffini LA, Sontheimer EJ (March 2010). "CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea". Nature Reviews Genetics 11 (3): 181–190. doi:10.1038/nrg2749. PMC 2928866. PMID 20125085.
- Redman, M; King, A; Watson, C; King, D (8 April 2016). "What is CRISPR/Cas9?". Archives of disease in childhood. Education and practice edition. PMID 27059283.
- Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (March 2007). "CRISPR provides acquired resistance against viruses in prokaryotes". Science 315 (5819): 1709–1712. Bibcode:2007Sci...315.1709B. doi:10.1126/science.1138140. PMID 17379808. (registration required)
- Marraffini LA, Sontheimer EJ (December 2008). "CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA". Science 322 (5909): 1843–1845. Bibcode:2008Sci...322.1843M. doi:10.1126/science.1165771. PMC 2695655. PMID 19095942.
- Grissa I, Vergnaud G, Pourcel C (2007). "The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats". BMC Bioinformatics 8: 172. doi:10.1186/1471-2105-8-172. PMC 1892036. PMID 17521438.
- http://www.nature.com/news/crispr-gene-editing-is-just-the-beginning-1.19510 Nature
- http://www.wired.com/2015/07/crispr-dna-editing-2/ Wired
- 2015 Breakthrough of the Year, Science Magazine, American Association for the Advancement of Science, 2016,
- Ledford, Heidi (3 June 2015). "CRISPR, the disruptor". News Feature. Nature 522 (7554).
- Snyder, Bill (21 August 2014). "New technique accelerates genome editing process". research news @ Vanderbilt. Nashville, Tennessee: Vanderbilt University.
- Hendel A, Bak RO, Clark JT, Kennedy AB, Ryan DE, Roy S, Steinfeld I, Lunstad BD, Kaiser RJ, Wilkens AB, Bacchetta R, Tsalenko A, Dellinger D, Bruhn L, Porteus MH (June 2015). "Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells". Nature Biotechnology 33: 985–9. doi:10.1038/nbt.3290. PMID 26121415.
- Mali P, Esvelt KM, Church GM (October 2013). "Cas9 as a versatile tool for engineering biology". Nature Methods 10 (10): 957–63. doi:10.1038/nmeth.2649. PMC 4051438. PMID 24076990.
- Ledford, Heidi (3 June 2015). "CRISPR, the disruptor". Nature 522 (7554): 20–24. doi:10.1038/522020a. PMID 26040877.
- Overballe-Petersen S, Harms K, Orlando LA, Mayar JV, Rasmussen S, Dahl TW, Rosing MT, Poole AM, Sicheritz-Ponten T, Brunak S, Inselmann S, de Vries J, Wackernagel W, Pybus OG, Nielsen R, Johnsen PJ, Nielsen KM, Willerslev E (December 2013). "Bacterial natural transformation by highly fragmented and damaged DNA". Proceedings of the National Academy of Sciences of the United States of America 110 (49): 19860–5. Bibcode:2013PNAS..11019860O. doi:10.1073/pnas.1315278110. PMID 24248361. Lay summary – Kurzweil (19 November 2013).
- Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A (Dec 1987). "Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product". Journal of Bacteriology 169 (12): 5429–33. PMC 213968. PMID 3316184.
- Lander ES (Jan 2016). "The Heroes of CRISPR". Cell 164 (1-2): 18–28. doi:10.1016/j.cell.2015.12.041. PMID 26771483.
- Mojica FJ, Díez-Villaseñor C, Soria E, Juez G (Apr 2000). "Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria". Molecular Microbiology 36 (1): 244–6. doi:10.1046/j.1365-2958.2000.01838.x. PMID 10760181.
- Jansen R, Embden JD, Gaastra W, Schouls LM (Mar 2002). "Identification of genes that are associated with DNA repeats in prokaryotes". Molecular Microbiology 43 (6): 1565–75. doi:10.1046/j.1365-2958.2002.02839.x. PMID 11952905.
- Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E (Feb 2005). "Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements". Journal of Molecular Evolution 60 (2): 174–82. doi:10.1007/s00239-004-0046-3. PMID 15791728.
- Pourcel C, Salvignol G, Vergnaud G (Mar 2005). "CRISPR elements in Yersinia pests acquire new repeats by preferential uptake of bacteriophage DNA and provide additional tools for evolutionary studies". Microbiology 151 (Pt 3): 653–63. doi:10.1099/mic.0.27437-0. PMID 15758212.
- Bolotin A, Quinquis B, Sorokin A, Ehrlich SD (Aug 2005). "Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin". Microbiology 151 (Pt 8): 2551–61. doi:10.1099/mic.0.28048-0. PMID 16079334.
- Pourcel C, Salvignol G, Vergnaud G (March 2005). "CRISPR elements in Yersinia pests acquire new repeats by preferential uptake of bacteriophage DNA and provide additional tools for evolutionary studies". Microbiology 151 (Pt 3): 653–663. doi:10.1099/mic.0.27437-0. PMID 15758212.
- Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E (February 2005). "Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements". Journal of Molecular Evolution 60 (2): 174–182. doi:10.1007/s00239-004-0046-3. PMID 15791728.
- Bolotin A, Quinquis B, Sorokin A, Ehrlich SD (August 2005). "Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin". Microbiology 151 (Pt 8): 2551–2561. doi:10.1099/mic.0.28048-0. PMID 16079334.
- Morange, M (June 2015). "What history tells us XXXVII. CRISPR-Cas: The discovery of an immune system in prokaryotes". Journal of Biosciences 2 (2): 221–223. doi:10.1007/s12038-015-9532-6. PMID 25963251.
- Pennisi E (August 2013). "The CRISPR craze". News Focus. Science 341 (6148): 833–836. doi:10.1126/science.341.6148.833. PMID 23970676.
- Cong, Le; Ran, F. Ann; Cox, David; Lin, Shuailiang; Barretto, Robert; Habib, Naomi; Hsu, Patrick D.; Wu, Xuebing; Jiang, Wenyan (2013-02-15). "Multiplex Genome Engineering Using CRISPR/Cas Systems". Science 339 (6121): 819–823. doi:10.1126/science.1231143. ISSN 0036-8075. PMC 3795411. PMID 23287718.
- Zhang, Feng (Aug 21, 2014), CRISPR-CAS Nickase Systems, Methods And Compositions For Sequence Manipulation in Eukaryotes, retrieved 2016-04-26
- DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM (Apr 2013). "Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems". Nucleic Acids Research 41 (7): 4336–43. doi:10.1093/nar/gkt135. PMC 3627607. PMID 23460208.
- Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK (Mar 2013). "Efficient genome editing in zebrafish using a CRISPR-Cas system". Nature Biotechnology 31 (3): 227–9. doi:10.1038/nbt.2501. PMC 3686313. PMID 23360964.
- Gratz SJ, Cummings AM, Nguyen JN, Hamm DC, Donohue LK, Harrison MM, Wildonger J, O'Connor-Giles KM (Aug 2013). "Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease". Genetics 194 (4): 1029–35. doi:10.1534/genetics.113.152710. PMC 3730909. PMID 23709638.
- Flowers GP, Timberlake AT, McLean KC, Monaghan JR, Crews CM (May 2014). "Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease". Development 141 (10): 2165–71. doi:10.1242/dev.105072. PMC 4011087. PMID 24764077.
- Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA (Aug 2013). "Heritable genome editing in C. elegans via a CRISPR-Cas9 system". Nature Methods 10 (8): 741–3. doi:10.1038/nmeth.2532. PMC 3822328. PMID 23817069.
- Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP (Nov 2013). "Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum, and rice". Nucleic Acids Research 41 (20): e188. doi:10.1093/nar/gkt780. PMC 3814374. PMID 23999092.
- Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R (May 2013). "One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering". Cell 153 (4): 910–8. doi:10.1016/j.cell.2013.04.025. PMID 23643243.
- Guo X, Li XJ (Jul 2015). "Targeted genome editing in primate embryos". Cell Research 25 (7): 767–8. doi:10.1038/cr.2015.64. PMID 26032266.
- Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M, Greely HT, Jinek M, Martin GS, Penhoet E, Puck J, Sternberg SH, Weissman JS, Yamamoto KR (2015). "Biotechnology. A prudent path forward for genomic engineering and germline gene modification". Science 348 (6230): 36–8. Bibcode:2015Sci...348...36B. doi:10.1126/science.aab1028. PMID 25791083.
- Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS (November 2013). "CRISPR interference (CRISPRi) for sequence-specific control of gene expression". Nature Protocols 8 (11): 2180–96. doi:10.1038/nprot.2013.132. PMID 24136345.
- Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (August 2012). "A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity". Science 337 (6096): 816–821. Bibcode:2012Sci...337..816J. doi:10.1126/science.1225829. PMID 22745249.
- Connor S (7 November 2013). "CRISPR gene therapy: Scientists call for more public debate around breakthrough technique". Science. London: The Independent. Retrieved 2013-11-25.
- Pollack A (11 May 2015). "Jennifer Doudna, a Pioneer Who Helped Simplify Genome Editing". The New York Times. Retrieved 12 May 2015.
- Young S (11 February 2014). "CRISPR and Other Genome Editing Tools Boost Medical Research and Gene Therapy’s Reach". MIT Technology Review (Cambridge, Massachusetts: Massachusetts Institute of Technology). Retrieved 2014-04-13.
- Haft DH, Selengut J, Mongodin EF, Nelson KE (November 2005). "A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes". PLoS Computational Biology 1 (6): e60. Bibcode:2005PLSCB...1...60H. doi:10.1371/journal.pcbi.0010060. PMC 1282333. PMID 16292354.
- Kunin V, Sorek R, Hugenholtz P (2007). "Evolutionary conservation of sequence and secondary structures in CRISPR repeats". Genome Biology 8 (4): R61. doi:10.1186/gb-2007-8-4-r61. PMC 1896005. PMID 17442114.
- Stern A, Keren L, Wurtzel O, Amitai G, Sorek R (August 2010). "Self-targeting by CRISPR: gene regulation or autoimmunity?". Trends in Genetics 26 (8): 335–340. doi:10.1016/j.tig.2010.05.008. PMC 2910793. PMID 20598393.
- Tyson GW, Banfield JF (January 2008). "Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses". Environmental Microbiology 10 (1): 200–207. doi:10.1111/j.1462-2920.2007.01444.x. PMID 17894817.
- Chylinski K, Makarova KS, Charpentier E, Koonin EV (June 2014). "Classification and evolution of type II CRISPR-Cas systems". Nucleic Acids Research 42 (10): 6091–105. doi:10.1093/nar/gku241. PMC 4041416. PMID 24728998.
- Wiedenheft B, Sternberg SH, Doudna JA (February 2012). "RNA-guided genetic silencing systems in bacteria and archaea". Nature 482 (7385): 331–8. Bibcode:2012Natur.482..331W. doi:10.1038/nature10886. PMID 22337052.
- Deng L, Garrett RA, Shah SA, Peng X, She Q (March 2013). "A novel interference mechanism by a type IIIB CRISPR-Cmr module in Sulfolobus". Molecular Microbiology 87 (5): 1088–99. doi:10.1111/mmi.12152. PMID 23320564.
- Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V (April 2011). "Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system". The EMBO Journal 30 (7): 1335–42. doi:10.1038/emboj.2011.41. PMC 3094125. PMID 21343909.
- Huo, Yanwu; Nam, Ki Hyun; Ding, Fang; Lee, Heejin; Wu, Lijie; Xiao, Yibei; Farchione, M Daniel; Zhou, Sharleen; Rajashankar, Kanagalaghatta. "Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation". Nature Structural & Molecular Biology 21 (9): 771–777. doi:10.1038/nsmb.2875. PMC 4156918. PMID 25132177.
- Aliyari R, Ding SW (January 2009). "RNA-based viral immunity initiated by the Dicer family of host immune receptors". Immunological Reviews 227 (1): 176–88. doi:10.1111/j.1600-065X.2008.00722.x. PMC 2676720. PMID 19120484.
- Cass SD, Haas KA, Stoll B, Alkhnbashi O, Sharma K, Urlaub H, Backofen R, Marchfelder A, Bolt EL (2015). "The role of Cas8 in type I CRISPR interference". Bioscience Reports 35 (3): e00197. doi:10.1042/BSR20150043. PMID 25940458.
- Makarova KS, Aravind L, Wolf YI, Koonin EV (2011). "Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems". Biology Direct 6: 38. doi:10.1186/1745-6150-6-38. PMC 3150331. PMID 21756346.
- Gasiunas G, Barrangou R, Horvath P, Siksnys V (September 2012). "Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria". Proceedings of the National Academy of Sciences of the United States of America 109 (39): E2579–E2586. Bibcode:2012PNAS..109E2579G. doi:10.1073/pnas.1208507109. PMC 3465414. PMID 22949671.
- Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA (March 2015). "Cas9 specifies functional viral targets during CRISPR-Cas adaptation". Nature 519 (7542): 199–202. Bibcode:2015Natur.519..199H. doi:10.1038/nature14245. PMC 4385744. PMID 25707807.
- Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong (2011-09-02). "Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity". The Journal of Biological Chemistry 286 (35): 30759–30768. doi:10.1074/jbc.M111.256263. ISSN 1083-351X. PMC 3162437. PMID 21697083.
- Chylinski K, Le Rhun A, Charpentier E (May 2013). "The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems". RNA Biology 10 (5): 726–37. doi:10.4161/rna.24321. PMC 3737331. PMID 23563642.
- Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM (May 2013). "High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates". PLoS Genetics 9 (5): e1003495. doi:10.1371/journal.pgen.1003495. PMC 3656092. PMID 23696746.
- Hatoum-Aslan A, Maniv I, Marraffini LA (Dec 2011). "Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site". Proceedings of the National Academy of Sciences of the United States of America 108 (52): 21218–22. Bibcode:2011PNAS..10821218H. doi:10.1073/pnas.1112832108. PMC 3248500. PMID 22160698.
- Yosef I, Goren MG, Qimron U (Jul 2012). "Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli". Nucleic Acids Research 40 (12): 5569–76. doi:10.1093/nar/gks216. PMC 3384332. PMID 22402487.
- Swarts DC, Mosterd C, van Passel MW, Brouns SJ (2012). "CRISPR interference directs strand specific spacer acquisition". PLOS ONE 7 (4): e35888. Bibcode:2012PLoSO...735888S. doi:10.1371/journal.pone.0035888. PMC 3338789. PMID 22558257.
- Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF (Jan 2011). "A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair". Molecular Microbiology 79 (2): 484–502. doi:10.1111/j.1365-2958.2010.07465.x. PMC 3071548. PMID 21219465.
- Han D, Lehmann K, Krauss G (Jun 2009). "SSO1450--a CAS1 protein from Sulfolobus solfataricus P2 with high affinity for RNA and DNA". FEBS Letters 583 (12): 1928–32. doi:10.1016/j.febslet.2009.04.047. PMID 19427858.
- Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA (Jun 2009). "Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense". Structure 17 (6): 904–12. doi:10.1016/j.str.2009.03.019. PMID 19523907.
- Beloglazova N, Brown G, Zimmerman MD, Proudfoot M, Makarova KS, Kudritska M, Kochinyan S, Wang S, Chruszcz M, Minor W, Koonin EV, Edwards AM, Savchenko A, Yakunin AF (Jul 2008). "A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats". The Journal of Biological Chemistry 283 (29): 20361–71. doi:10.1074/jbc.M803225200. PMC 2459268. PMID 18482976.
- Samai P, Smith P, Shuman S (Dec 2010). "Structure of a CRISPR-associated protein Cas2 from Desulfovibrio vulgaris". Acta Crystallographica. Section F, Structural Biology and Crystallization Communications 66 (Pt 12): 1552–6. doi:10.1107/S1744309110039801. PMC 2998353. PMID 21139194.
- Nam KH, Ding F, Haitjema C, Huang Q, DeLisa MP, Ke A (Oct 2012). "Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein". The Journal of Biological Chemistry 287 (43): 35943–52. doi:10.1074/jbc.M112.382598. PMC 3476262. PMID 22942283.
- Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA (2014). "Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity". Nat. Struct. Mol. Biol. 21 (6): 528–34. doi:10.1038/nsmb.2820. PMC 4075942. PMID 24793649.
- Nuñez JK, Lee AS, Engelman A, Doudna JA (2015). "Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity". Nature 519 (7542): 193–8. doi:10.1038/nature14237. PMC 4359072. PMID 25707795.
- Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y (2015). "Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems". Cell 163 (4): 840–53. doi:10.1016/j.cell.2015.10.008. PMID 26478180.
- Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA (2015). "Foreign DNA capture during CRISPR-Cas adaptive immunity". Nature 527 (7579): 535–8. doi:10.1038/nature15760. PMID 26503043.
- Horvath P, Romero DA, Coûté-Monvoisin AC, Richards M, Deveau H, Moineau S, Boyaval P, Fremaux C, Barrangou R (Feb 2008). "Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus". Journal of Bacteriology 190 (4): 1401–1412. doi:10.1128/JB.01415-07. PMC 2238196. PMID 18065539.
- Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, Boyaval P, Romero DA, Horvath P, Moineau S (Feb 2008). "Phage response to CRISPR-encoded resistance in Streptococcus thermophilus". Journal of Bacteriology 190 (4): 1390–1400. doi:10.1128/JB.01412-07. PMC 2238228. PMID 18065545.
- Mojica FJ, Díez-Villaseñor C, García-Martínez J, Almendros C (Mar 2009). "Short motif sequences determine the targets of the prokaryotic CRISPR defence system". Microbiology 155 (Pt 3): 733–740. doi:10.1099/mic.0.023960-0. PMID 19246744.
- Lillestøl RK, Shah SA, Brügger K, Redder P, Phan H, Christiansen J, Garrett RA (Apr 2009). "CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties". Molecular Microbiology 72 (1): 259–272. doi:10.1111/j.1365-2958.2009.06641.x. PMID 19239620.
- Shah SA, Hansen NR, Garrett RA (Feb 2009). "Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism". Biochemical Society Transactions 37 (Pt 1): 23–28. doi:10.1042/BST0370023. PMID 19143596.
- Díez-Villaseñor C, Guzmán NM, Almendros C, García-Martínez J, Mojica FJ (May 2013). "CRISPR-spacer integration reporter plasmids reveal distinct genuine acquisition specificities among CRISPR-Cas I-E variants of Escherichia coli". RNA Biology 10 (5): 792–802. doi:10.4161/rna.24023. PMC 3737337. PMID 23445770.
- Erdmann S, Garrett RA (Sep 2012). "Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms". Molecular Microbiology 85 (6): 1044–56. doi:10.1111/j.1365-2958.2012.08171.x. PMC 3468723. PMID 22834906.
- Shah SA, Erdmann S, Mojica FJ, Garrett RA (May 2013). "Protospacer recognition motifs: mixed identities and functional diversity". RNA Biology 10 (5): 891–9. doi:10.4161/rna.23764. PMC 3737346. PMID 23403393.
- Andersson AF, Banfield JF (May 2008). "Virus population dynamics and acquired virus resistance in natural microbial communities". Science 320 (5879): 1047–1050. Bibcode:2008Sci...320.1047A. doi:10.1126/science.1157358. PMID 18497291.
- Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA (Jan 2011). "Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time". Genome Research 21 (1): 126–36. doi:10.1101/gr.111732.110. PMC 3012920. PMID 21149389.
- Goren MG, Yosef I, Auster O, Qimron U (Oct 2012). "Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli". Journal of Molecular Biology 423 (1): 14–6. doi:10.1016/j.jmb.2012.06.037. PMID 22771574.
- Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E (2012). "Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system". Nature Communications 3: 945. Bibcode:2012NatCo...3E.945D. doi:10.1038/ncomms1937. PMID 22781758.
- Gesner EM, Schellenberg MJ, Garside EL, George MM, Macmillan AM (Jun 2011). "Recognition and maturation of effector RNAs in a CRISPR interference pathway". Nature Structural & Molecular Biology 18 (6): 688–92. doi:10.1038/nsmb.2042. PMID 21572444.
- Sashital DG, Jinek M, Doudna JA (Jun 2011). "An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3". Nature Structural & Molecular Biology 18 (6): 680–7. doi:10.1038/nsmb.2043. PMID 21572442.
- Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA (Sep 2010). "Sequence- and structure-specific RNA processing by a CRISPR endonuclease". Science 329 (5997): 1355–8. Bibcode:2010Sci...329.1355H. doi:10.1126/science.1192272. PMC 3133607. PMID 20829488.
- Carte J, Wang R, Li H, Terns RM, Terns MP (Dec 2008). "Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes". Genes & Development 22 (24): 3489–3496. doi:10.1101/gad.1742908. PMC 2607076. PMID 19141480.
- Wang R, Preamplume G, Terns MP, Terns RM, Li H (Feb 2011). "Interaction of the Cas6 riboendonuclease with CRISPR RNAs: recognition and cleavage". Structure 19 (2): 257–64. doi:10.1016/j.str.2010.11.014. PMC 3154685. PMID 21300293.
- Niewoehner O, Jinek M, Doudna JA (Jan 2014). "Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases". Nucleic Acids Research 42 (2): 1341–53. doi:10.1093/nar/gkt922. PMC 3902920. PMID 24150936.
- Garneau JE, Dupuis MÈ, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S (Nov 2010). "The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA". Nature 468 (7320): 67–71. Bibcode:2010Natur.468...67G. doi:10.1038/nature09523. PMID 21048762.
- Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJ, Severinov K (Jun 2011). "Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence". Proceedings of the National Academy of Sciences of the United States of America 108 (25): 10098–103. Bibcode:2011PNAS..10810098S. doi:10.1073/pnas.1104144108. PMC 3121866. PMID 21646539.
- Gudbergsdottir S, Deng L, Chen Z, Jensen JV, Jensen LR, She Q, Garrett RA (Jan 2011). "Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers". Molecular Microbiology 79 (1): 35–49. doi:10.1111/j.1365-2958.2010.07452.x. PMC 3025118. PMID 21166892.
- Manica A, Zebec Z, Teichmann D, Schleper C (Apr 2011). "In vivo activity of CRISPR-mediated virus defence in a hyperthermophilic archaeon". Molecular Microbiology 80 (2): 481–91. doi:10.1111/j.1365-2958.2011.07586.x. PMID 21385233.
- Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ (May 2011). "Structural basis for CRISPR RNA-guided DNA recognition by Cascade". Nature Structural & Molecular Biology 18 (5): 529–36. doi:10.1038/nsmb.2019. PMID 21460843.
- Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, Doudna JA, Nogales E (Sep 2011). "Structures of the RNA-guided surveillance complex from a bacterial immune system". Nature 477 (7365): 486–9. Bibcode:2011Natur.477..486W. doi:10.1038/nature10402. PMID 21938068.
- Zhang J, Rouillon C, Kerou M, Reeks J, Brugger K, Graham S, Reimann J, Cannone G, Liu H, Albers SV, Naismith JH, Spagnolo L, White MF (Feb 2012). "Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity". Molecular Cell 45 (3): 303–13. doi:10.1016/j.molcel.2011.12.013. PMC 3381847. PMID 22227115.
- Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP (Nov 2009). "RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex". Cell 139 (5): 945–956. doi:10.1016/j.cell.2009.07.040. PMC 2951265. PMID 19945378.
- Marraffini LA, Sontheimer EJ (Jan 2010). "Self versus non-self discrimination during CRISPR RNA-directed immunity". Nature 463 (7280): 568–571. Bibcode:2010Natur.463..568M. doi:10.1038/nature08703. PMC 2813891. PMID 20072129.
- "Scientists successfully edit human immune-system T cells | KurzweilAI". www.kurzweilai.net. Retrieved 2016-01-01.
- Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A (Aug 2015). "Generation of knock-in primary human T cells using Cas9 ribonucleoproteins". Proceedings of the National Academy of Sciences of the United States of America 112 (33): 10437–42. doi:10.1073/pnas.1512503112. PMC 4547290. PMID 26216948.
- Touchon M, Rocha EP (2010). Randau L, ed. "The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella". PLOS ONE 5 (6): e11126. Bibcode:2010PLoSO...511126T. doi:10.1371/journal.pone.0011126. PMC 2886076. PMID 20559554.
- Rho M, Wu YW, Tang H, Doak TG, Ye Y (2012). "Diverse CRISPRs evolving in human microbiomes". PLoS Genetics 8 (6): e1002441. doi:10.1371/journal.pgen.1002441. PMC 3374615. PMID 22719260.
- Sun CL, Barrangou R, Thomas BC, Horvath P, Fremaux C, Banfield JF (Feb 2013). "Phage mutations in response to CRISPR diversification in a bacterial population". Environmental Microbiology 15 (2): 463–70. doi:10.1111/j.1462-2920.2012.02879.x. PMID 23057534.
- Kuno S, Sako Y, Yoshida T (May 2014). "Diversification of CRISPR within coexisting genotypes in a natural population of the bloom-forming cyanobacterium Microcystis aeruginosa". Microbiology 160 (Pt 5): 903–16. doi:10.1099/mic.0.073494-0. PMID 24586036.
- Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P (2007). "CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats". BMC Bioinformatics 8: 209. doi:10.1186/1471-2105-8-209. PMC 1924867. PMID 17577412.
- Edgar RC (2007). "PILER-CR: fast and accurate identification of CRISPR repeats". BMC Bioinformatics 8: 18. doi:10.1186/1471-2105-8-18. PMC 1790904. PMID 17239253.
- Grissa I, Vergnaud G, Pourcel C (Jul 2007). "CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats". Nucleic Acids Research 35 (Web Server issue): W52–7. doi:10.1093/nar/gkm360. PMC 1933234. PMID 17537822.
- Pride DT, Salzman J, Relman DA (Sep 2012). "Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses". Environmental Microbiology 14 (9): 2564–76. doi:10.1111/j.1462-2920.2012.02775.x. PMC 3424356. PMID 22583485.
- Held NL, Herrera A, Whitaker RJ (Apr 2013). "Reassortment of CRISPR repeat-spacer loci in Sulfolobus islandicus". Environmental Microbiology. doi:10.1111/1462-2920.12146. PMID 23701169.
- Held NL, Herrera A, Cadillo-Quiroz H, Whitaker RJ (2010). "CRISPR associated diversity within a population of Sulfolobus islandicus". PLOS ONE 5 (9): e12988. Bibcode:2010PLoSO...512988H. doi:10.1371/journal.pone.0012988. PMC 2946923. PMID 20927396.
- Skennerton CT, Imelfort M, Tyson GW (May 2013). "Crass: identification and reconstruction of CRISPR from unassembled metagenomic data". Nucleic Acids Research 41 (10): e105. doi:10.1093/nar/gkt183. PMC 3664793. PMID 23511966.
- Stern A, Mick E, Tirosh I, Sagy O, Sorek R (Oct 2012). "CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome". Genome Research 22 (10): 1985–94. doi:10.1101/gr.138297.112. PMC 3460193. PMID 22732228.
- Koonin EV, Wolf YI (2009). "Is evolution Darwinian or/and Lamarckian?". Biology Direct 4: 42. doi:10.1186/1745-6150-4-42. PMC 2781790. PMID 19906303.
- Weiss A (2015). "Lamarckian Illusions". Trends in Ecology & Evolution 30 (10): 566–568. doi:10.1016/j.tree.2015.08.003. PMID 26411613.
- Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D (2009). Ahmed N, ed. "Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes". PLOS ONE 4 (1): e4169. Bibcode:2009PLoSO...4.4169H. doi:10.1371/journal.pone.0004169. PMC 2612747. PMID 19132092.
- Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS (May 2013). "A CRISPR/Cas system mediates bacterial innate immune evasion and virulence". Nature 497 (7448): 254–7. Bibcode:2013Natur.497..254S. doi:10.1038/nature12048. PMC 3651764. PMID 23584588.
- Novick RP, Christie GE, Penadés JR (Aug 2010). "The phage-related chromosomal islands of Gram-positive bacteria". Nature Reviews. Microbiology 8 (8): 541–551. doi:10.1038/nrmicro2393. PMC 3522866. PMID 20634809.
- Seed KD, Lazinski DW, Calderwood SB, Camilli A (Feb 2013). "A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity". Nature 494 (7438): 489–491. Bibcode:2013Natur.494..489S. doi:10.1038/nature11927. PMC 3587790. PMID 23446421.
- Ledford H (2015). "CRISPR, the disruptor". Nature 522 (7554): 20–4. Bibcode:2015Natur.522...20L. doi:10.1038/522020a. PMID 26040877.
- "CRISPR/Cas9 Plasmids". www.systembio.com. Retrieved 2015-12-17.
- "CRISPR Cas9 Genome Editing". www.origene.com. OriGene. Retrieved 2015-12-17.
- Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F (Nov 2013). "Genome engineering using the CRISPR-Cas9 system". Nature Protocols 8 (11): 2281–308. doi:10.1038/nprot.2013.143. PMC 3969860. PMID 24157548.
- Horvath P, Barrangou R (Jan 2010). "CRISPR/Cas, the immune system of bacteria and archaea". Science 327 (5962): 167–70. doi:10.1126/science.1179555. PMID 20056882.
- Bialk P, Rivera-Torres N, Strouse B, Kmiec EB (2015-06-08). "Regulation of Gene Editing Activity Directed by Single-Stranded Oligonucleotides and CRISPR/Cas9 Systems". PLOS ONE 10 (6): e0129308. doi:10.1371/journal.pone.0129308. PMC 4459703. PMID 26053390.
- "Optimized CRISPR Design". crispr.mit.edu. Retrieved 2015-12-20.
- Carl Zimmerman (Oct 15, 2015). "Editing of Pig DNA May Lead to More Organs for People". NY Times.
- Hale CR, Majumdar S, Elmore J, Pfister N, Compton M, Olson S, Resch AM, Glover CV, Graveley BR, Terns RM, Terns MP (Feb 2012). "Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs". Molecular Cell 45 (3): 292–302. doi:10.1016/j.molcel.2011.10.023. PMC 3278580. PMID 22227116.
- Sorek R, Kunin V, Hugenholtz P (Mar 2008). "CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea". Nature Reviews. Microbiology 6 (3): 181–186. doi:10.1038/nrmicro1793. PMID 18157154.
- Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (Feb 2013). "Multiplex genome engineering using CRISPR/Cas systems". Science 339 (6121): 819–823. Bibcode:2013Sci...339..819C. doi:10.1126/science.1231143. PMC 3795411. PMID 23287718.
- Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM (Feb 2013). "RNA-guided human genome engineering via Cas9". Science 339 (6121): 823–826. Bibcode:2013Sci...339..823M. doi:10.1126/science.1232033. PMC 3712628. PMID 23287722.
Hou Z, Zhang Y, Propson NE, Howden SE, Chu LF, Sontheimer EJ, Thomson JA (Sep 2013). "Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis". Proceedings of the National Academy of Sciences of the United States of America 110 (39): 15644–15649. Bibcode:2013PNAS..11015644H. doi:10.1073/pnas.1313587110.
- Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F (2014). "Genome-scale CRISPR-Cas9 knockout screening in human cells". Science 343 (6166): 84–7. doi:10.1126/science.1247005. PMC 4089965. PMID 24336571.
- van Erp PB, Bloomer G, Wilkinson R, Wiedenheft B (2015). "The history and market impact of CRISPR RNA-guided nucleases". Curr Opin Virol 12: 85–90. doi:10.1016/j.coviro.2015.03.011. PMID 25914022.
- Maggio I, Gonçalves MA (2015). "Genome editing at the crossroads of delivery, specificity, and fidelity". Trends Biotechnol. 33 (5): 280–91. doi:10.1016/j.tibtech.2015.02.011. PMID 25819765.
- Rath D, Amlinger L, Rath A, Lundgren M (2015). "The CRISPR-Cas immune system: Biology, mechanisms and applications". Biochimie 117: 119–28. doi:10.1016/j.biochi.2015.03.025. PMID 25868999.
- Freedman BS, Brooks CR, Lam AQ, Fu H, Morizane R, Agrawal V, Saad AF, Li MK, Hughes MR, Werff RV, Peters DT, Lu J, Baccei A, Siedlecki AM, Valerius MT, Musunuru K, McNagny KM, Steinman TI, Zhou J, Lerou PH, Bonventre JV (23 October 2015). "Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids". Nature Communications 6: 8715. doi:10.1038/ncomms9715. PMID 26493500.
- Bellin M, Casini S, Davis RP, D'Aniello C, Haas J, Ward-van Oostwaard D, Tertoolen LG, Jung CB, Elliott DA, Welling A, Laugwitz KL, Moretti A, Mummery CL (Dec 2013). "Isogenic human pluripotent stem cell pairs reveal the role of a KCNH2 mutation in long-QT syndrome". The EMBO Journal 32 (24): 3161–75. doi:10.1038/emboj.2013.240. PMC 3981141. PMID 24213244.
- Science News Staff (December 17, 2015). "And Science’s Breakthrough of the Year is …". news.sciencemag.org. Retrieved 2015-12-21.
- Citorik, Robert J; Mimee, Mark; Lu, Timothy K (2014). "Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases". Nature Biotechnology 32 (11): 1141–1145. doi:10.1038/nbt.3011. ISSN 1087-0156.
- Abrahimi, Parwiz; Chang, William G.; Kluger, Martin S.; Qyang, Yibing; Tellides, George; Saltzman, W. Mark; Pober, Jordan S. (2015-07-03). "Efficient gene disruption in cultured primary human endothelial cells by CRISPR/Cas9". Circulation Research. doi:10.1161/CIRCRESAHA.117.306290. ISSN 1524-4571. PMID 25940550.
- Yong, Ed (2015-11-25). "The Revolutionary Gene-Editing Technique That Reveals Cancer’s Weaknesses". The Atlantic. Retrieved 2016-02-21.
- "Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications". Pubmed. 2016-03-04. PMID 26944702. Retrieved 2016-05-22.
- "Who Owns the Biggest Biotech Discovery of the Century? There’s a bitter fight over the patents for CRISPR, a breakthrough new form of DNA editing.". MIT Technology Review. Retrieved 25 February 2015.
CRISPR Patents Spark Fight to Control Genome Editing
- Fye, Shaan. "Genetic Rough Draft: Editas and CRISPR". The Atlas Business Journal. Retrieved 19 January 2016.
- "CRISPR Madness". GEN.
- Antonio Regalado for MIT Technology Review, March 5, 2015 Engineering the Perfect Baby
- Lanphier E, Urnov F, Haecker SE, Werner M, Smolenski J (2015). "Don't edit the human germ line". Nature 519 (7544): 410–1. Bibcode:2015Natur.519..410L. doi:10.1038/519410a. PMID 25810189.
- Wade, Nicholas (19 March 2015). "Scientists Seek Ban on Method of Editing the Human Genome". The New York Times. Retrieved 20 March 2015.
The biologists writing in Science support continuing laboratory research with the technique, and few if any scientists believe it is ready for clinical use.
- Liang P, Xu Y, Zhang X, Ding C, Huang R, Zhang Z, Lv J, Xie X, Chen Y, Li Y, Sun Y, Bai Y, Songyang Z, Ma W, Zhou C, Huang J (2015). "CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes". Protein Cell 6 (5): 363–72. doi:10.1007/s13238-015-0153-5. PMC 4417674. PMID 25894090.
- Kolata, Gina (23 April 2015). "Chinese Scientists Edit Genes of Human Embryos, Raising Concerns". The New York Times. Retrieved 24 April 2015.
- "Chinese scientists genetically modify human embryos". Nature. 22 April 2015.
- "International Summit on Gene Editing". National Academies of Sciences, Engineering, and Medicine. 3 December 2015. Retrieved 3 December 2015.
- Gallagher, James (1 February 2016). "Scientists get 'gene editing' go-ahead". BBC News (BBC). Retrieved 1 February 2016.
- Cheng, Maria (1 February 2016). "Britain approves controversial gene-editing technique". AP News. Retrieved 1 February 2016.
- Mulepati, Sabin. Personal Interview. 5 April 2016.
- Talbot, Da\vid (2016). "Precise Gene Editing in Plants/ 10 Breakthrough Technologies 2016". Massachusetts Institute of Technology. Retrieved 18 March 2016.
- Larson, Christina; Schaffer, Amanda (2014). "Genome Editing/ 10 Breakthrough Technologies 2014". Massachusetts Institute of Technology. Retrieved 18 March 2016.
- Huo, Yanwu; Nam, Ki Hyun; Ding, Fang; Lee, Heejin; Wu, Lijie; Xiao, Yibei; Farchione, M Daniel; Zhou, Sharleen; Rajashankar, Kanagalaghatta; Kurinov, Igor; Zhang, Rongguang; Ke, Ailong (17 August 2014). "Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation". Nature Structural & Molecular Biology 21 (9): 771–777. doi:10.1038/nsmb.2875. PMC 4156918. PMID 25132177.
- CRISPR-Cas: A Laboratory Manual Edited by Jennifer Doudna, University of California, Berkeley; Prashant Mali, University of California, San Diego
- Sander JD, Joung JK (Apr 2014). "CRISPR-Cas systems for editing, regulating and targeting genomes". Nature Biotechnology 32 (4): 347–55. doi:10.1038/nbt.2842. PMID 24584096.
- Ian M. Slaymaker, Linyi Gao, Bernd Zetsche, David A. Scott, Winston X. Yan, and Feng Zhang (2015). "Rationally engineered Cas9 nucleases with improved specificity". Science: Published online. doi:10.1126/science.aad5227.
- Terns RM, Terns MP (Mar 2014). "CRISPR-based technologies: prokaryotic defense weapons repurposed". Trends in Genetics 30 (3): 111–8. doi:10.1016/j.tig.2014.01.003. PMID 24555991.
- Westra ER, Buckling A, Fineran PC (May 2014). "CRISPR-Cas systems: beyond adaptive immunity". Nature Reviews. Microbiology 12 (5): 317–26. doi:10.1038/nrmicro3241. PMID 24704746.
- Andersson AF, Banfield JF (May 2008). "Virus population dynamics and acquired virus resistance in natural microbial communities". Science 320 (5879): 1047–1050. Bibcode:2008Sci...320.1047A. doi:10.1126/science.1157358. PMID 18497291.
- Hale C, Kleppe K, Terns RM, Terns MP (Dec 2008). "Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus". RNA 14 (12): 2572–2579. doi:10.1261/rna.1246808. PMC 2590957. PMID 18971321.
- van der Ploeg JR (Jun 2009). "Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages". Microbiology 155 (Pt 6): 1966–1976. doi:10.1099/mic.0.027508-0. PMID 19383692.
- van der Oost J, Brouns SJ (Nov 2009). "RNAi: prokaryotes get in on the act". Cell 139 (5): 863–865. doi:10.1016/j.cell.2009.11.018. PMID 19945373.
- Karginov FV, Hannon GJ (Jan 2010). "The CRISPR system: small RNA-guided defense in bacteria and archaea". Molecular Cell 37 (1): 7–19. doi:10.1016/j.molcel.2009.12.033. PMC 2819186. PMID 20129051.
- Pul U, Wurm R, Arslan Z, Geissen R, Hofmann N, Wagner R (Mar 2010). "Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS". Molecular Microbiology 75 (6): 1495–1512. doi:10.1111/j.1365-2958.2010.07073.x. PMID 20132443.
- Díez-Villaseñor C, Almendros C, García-Martínez J, Mojica FJ (May 2010). "Diversity of CRISPR loci in Escherichia coli". Microbiology 156 (Pt 5): 1351–1361. doi:10.1099/mic.0.036046-0. PMID 20133361.
- Deveau H, Garneau JE, Moineau S (2010). "CRISPR/Cas system and its role in phage-bacteria interactions". Annual Review of Microbiology 64: 475–493. doi:10.1146/annurev.micro.112408.134123. PMID 20528693.
- Koonin EV, Makarova KS (Dec 2009). "CRISPR-Cas: an adaptive immunity system in prokaryotes". F1000 Biology Reports 1: 95. doi:10.3410/B1-95. PMC 2884157. PMID 20556198.
- "The age of the red pen". The Economist. August 22, 2015. ISSN 0013-0613. Retrieved 2015-08-25.
- Lander, E. S. (2016). "The Heroes of CRISPR". Cell 164 (1-2): 18–28. doi:10.1016/j.cell.2015.12.041. PMID 26771483.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
CRISPR associated protein Provide feedback
This domain forms an anti-parallel beta strand structure with flanking alpha helical regions.
This tab holds annotation information from the InterPro database.
InterPro entry IPR010179
The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA.
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes [PUBMED:17442114]. CRISPRs appear to provide acquired resistance against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).
The defense reaction is divided into three stages. In the adaptation stage, the invader DNA is cleaved, and a piece of it is selected to be integrated as a new spacer into the CRISPR locus, where it is stored as an identity tag for future attacks by this invader. During the second stage (the expression stage), the CRISPR RNA (pre-crRNA) is transcribed and subsequently processed into the mature crRNAs. In the third stage (the interference stage), Cas proteins, together with crRNAs, identify and degrade the invader [PUBMED:17379808, PUBMED:16545108, PUBMED:21699496].
The CRISPR-Cas systems have been sorted into three major classes. In CRISPR-Cas types I and III, the mature crRNA is generally generated by a member of the Cas6 protein family. Whereas in system III the Cas6 protein acts alone, in some class I systems it is part of a complex of Cas proteins known as Cascade (CRISPR-associated complex for antiviral defense). The Cas6 protein is necessary for crRNA production whereas the additional Cas proteins that form the Cascade complex are needed for crRNA stability [PUBMED:24459147].
This entry represents the Cse3 (CRISPR/Cas Subtype Ecoli protein 3) family of Cas proteins. The Thermus thermophilus HB8 family member has been crystallised and found to have a structure consisting of two domains with opposing parallel beta-sheets, known as a beta-sheet platform [PUBMED:16672237]. This structure is similar to those found in the sex-lethal protein and poly(A)-binding protein and is consistent with an RNA-binding function.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats . It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation . Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers .
The clan contains the following 7 members:Cas6 Cas_Cas5d Cas_Cas6 Cas_Cmr3 CRISPR_assoc DUF2276 RAMPs
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Number in seed:||114|
|Number in full:||180|
|Average length of the domain:||218.60 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||97.26 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CRISPR_assoc domain has been found. There are 20 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
Loading structure mapping...