CRISPR-Cas systems

Extracted Attributes

• Nature

  Adaptive immune system in prokaryotes

• Classes

  Class 1 (multisubunit effector complexes), Class 2 (single large multidomain protein effector)

• Found in

  Bacteria (~50% of sequenced genomes), Archaea (~90% of sequenced genomes)

• Mechanism

  DNA/RNA-guided cleavage by Cas enzymes

• Components

  CRISPR repeat-spacer arrays, Cas genes/proteins (e.g., Cas9, Cas13, Cas12a, Cas14)

• Recent Innovation

  OpenCrisper-1 (open-source AI gene editor)

• OpenCrisper-1 Technology

  AI and protein language models

• Developer of OpenCrisper-1

  Profluent Bio

• Nobel Prize in Chemistry Year

  2020

Timeline

• The Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for the development of the CRISPR-Cas9 genome editing technique. (Source: Summary, Wikipedia)

  2020-10-07

CRISPR

CRISPR (; acronym of clustered regularly interspaced short palindromic repeats) is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic CRISPR is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral (i.e. anti-phage) defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea. Cas9 (or "CRISPR-associated protein 9") is an enzyme that uses CRISPR sequences as a guide to recognize and open up specific strands of DNA that are complementary to the CRISPR sequence. Cas9 enzymes together with CRISPR sequences form the basis of a technology known as CRISPR-Cas9 that can be used to edit genes within living organisms. This editing process has a wide variety of applications including basic biological research, development of biotechnological products, and treatment of diseases. The development of the CRISPR-Cas9 genome editing technique was recognized by the Nobel Prize in Chemistry in 2020 awarded to Emmanuelle Charpentier and Jennifer Doudna.

Web Search Results

• Origins and evolution of CRISPR-Cas systems - Journals

  The CRISPR-Cas systems are a universal immune mechanism that, at least in principle, can adapt to defend the host from any MGE. Because of this universal adaptability, CRISPR-Cas systems do diversify as extensively as innate immune systems, such as restriction-modification modules, the ubiquitous and most abundant defence component in archaea and bacteria. Nevertheless, the Cas protein sequences and the genomic organization of CRISPR-cas loci display substantial diversity. All CRISPR-Cas [...] systems are divided into two distinct classes, on the basis of the design principles of the effector modules. Class 1 systems have multisubunit effector complexes comprising several Cas proteins, whereas in class 2 systems, the effector is a single, large, multidomain protein (figure 1). Classification of CRISPR-Cas systems is a complicated matter. There are no universal Cas proteins that could be used as phylogenetic markers, and even the phylogeny of the most evolutionarily conserved [...] Along with eukaryotic RNA interference (RNAi) and prokaryotic Argonaute-centred defence mechanisms, the CRISPR-Cas belong to nucleic acid-guided defence systems [14–18]. Arguably, among these mechanisms, CRISPR-Cas systems are the most biologically complex because, in contrast with the innate immunity mechanisms, such as those of the Argonaute-based systems and most of the forms of eukaryotic RNAi, but similarly to the piRNA branch of RNAi, CRISPR-Cas possess an integral capacity of creating

• CRISPR-Cas systems: Overview, innovations and applications in ...

  So far, as a rapid and efficient genome editing tool, CRISPR-Cas systems have been extensively used in a variety of species, including bacteria, yeast, tobacco, Arabidopsis, sorghum, rice, Caenorhabditis elegans, Drosophila, zebrafish, Xenopus laevis, mouse, rat, rabbit, dog, sheep, pig and monkey ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( as well as various human cell lines, such as tumor cells, adult cells and stem cells ( ( In medical field, the most important application of CRISPR-Cas systems is to [...] In addition to editing DNA, CRISPR-Cas systems can also edit RNA. Class 2 Type VI CRISPR-Cas13 systems contain a single RNA-guided Cas13 protein with ribonuclease activity, which can bind to target single-stranded RNA (ssRNA) and specifically cleave the target ( To date, four Cas13 proteins have been identified: Cas13a (also known as C2c2), Cas13b, Cas13c and Cas13d ( They have successfully been applied in RNA knockdown, transcript labeling, splicing regulation and virus detection ( ( ( Later, [...] CRISPR-Cas is an adaptive immune system existing in most bacteria and archaea, preventing them from being infected by phages, viruses and other foreign genetic elements ( ( It is composed of CRISPR repeat-spacer arrays, which can be further transcribed into CRISPR RNA (crRNA) and _trans_-activating CRISPR RNA (tracrRNA), and a set of CRISPR-associated (cas) genes which encode Cas proteins with endonuclease activity ( When the prokaryotes are invaded by foreign genetic elements, the foreign DNA

• CRISPR/Cas systems: Delivery and application in gene therapy

  The CRISPR/Ca systems, as the most popular gene editing tool, can mediate multifunctional and high-precision genome modification, realizing the treatment of a variety of major diseases such as tumors, genetic diseases, and infectious diseases. Normally, the CRISPR/Cas system needs delivery strategies including \_in vitro\_, \_in vivo\_, and \_ex vivo\_ to exert its function in disease treatment. A very necessary prerequisite for the function of the CRISPR/Cas9 system is efficient delivery to [...] \\FIGURE 2\\. Gene editing schematic of four commonly used CRISPR/Cas systems (Cas9, Cas12a, Cas13a, and Cas14). \\(A)\\ CRISPR/Cas9 system is able to cleave at 3bp upstream of the double stranded DNA (dsDNA) PAM by the guidance of small guide RNA (sgRNA) (crRNA: tracrRNA), resulting in the double strand break (DSB) of the target site and the blunt ends. \\(B)\\ CRISPR/Cas12a system only depends on crRNA to recognize the PAM of dsDNA, then cleaves the target DNA in turn to produce sticky ends [...] cleavage of the target (Makarova et al., 2015). The Class 1 CRISPR/Cas system is rarely applied in eukaryotic gene engineering due to the comparatively difficult heterologous expression of multiple groups of hierarchically linked complexes (Makarova et al., 2015). The Class 2 CRISPR/Cas system is widely used in basic and translational biomedical research due to the advantages of single nuclease application. As summarized in Figure 2, Class 2 CRISPR/Cas system is the common genome editing tool

• CRISPR - Wikipedia

  CRISPR-Cas systems fall into two classes. Class 1 systems use a complex of multiple Cas proteins to degrade foreign nucleic acids. Class 2 systems use a single large Cas protein for the same purpose. Class 1 is divided into types I, III, and IV; class 2 is divided into types II, V, and VI. The 6 system types are divided into 33 subtypes. Each type and most subtypes are characterized by a "signature gene" found almost exclusively in the category. Classification is also based on the complement of [...] cas genes that are present. Most CRISPR-Cas systems have a Cas1 protein. The phylogeny of Cas1 proteins generally agrees with the classification system, but exceptions exist due to module shuffling. 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. [...] ### CRISPR-associated systems [edit] A major advance in understanding CRISPR came with Jansen's observation that the prokaryote repeat cluster was accompanied by four homologous genes that make up CRISPR-associated systems, cas 1–4. The Cas proteins showed helicase and nuclease motifs, suggesting a role in the dynamic structure of the CRISPR loci. In this publication, the acronym CRISPR was used as the universal name of this pattern, but its function remained enigmatic.

• Mechanism and Applications of CRISPR/Cas-9-Mediated Genome ...

  Based on the structure and functions of Cas-proteins, CRISPR/Cas system can be divided into Class I (type I, III, and IV) and Class II (type II, V, and VI). The class I systems consist of multi-subunit Cas-protein complexes, while the class II systems utilize a single Cas-protein. Since the structure of type II CRISPR/Cas-9 is relatively simple, it has been well studied and extensively used in genetic engineering.10 Guide RNA (gRNA) and CRISPR-associated (Cas-9) proteins are the two essential [...] Moreover, the latest researches show that the CRISPR/Cas-mediated single-base editing and prime editing systems can directly install mutations in cellular DNA without the need for a donor template. The CRISPR/Cas-base editor and prime editor system do not produce DSB, which reduces the possibility of indels that are different from conventional Cas-9.38 So far, two types of base editors have been developed: cytosine base editor (CBE) and adenine base editor (ABE).39 The CBE is a type of base [...] CRISPR/Cas system. They are a recently discovered method to reduce off-target effects of CRISPR/Cas-9.74 From Acr proteins, AcrIIA4 specifically targets Cas-9 nuclease. AcrIIA4 mimics DNA and binds to the Cas-9 site, making impossible to perform further cleavage in area outside the target region.75 Furthermore, CRISPR/Cas-9 gene editing has been challenged by ethics and safety all over the world. Since the technology is still in its infancy and knowledge about the genome is limited, many