CRISPR/Cpf1

Clustered Regularly Interspaced Short Palindromic Repeats from Prevotella and Francisella 1 or CRISPR/Cpf1 is a DNA-editing technology analogous to the CRISPR/Cas9 system. Cpf1 is an RNA-guided endonuclease of a class II CRISPR/Cas system. This acquired immune mechanism is found in Prevotella and Francisella bacteria. It prevents genetic damage from viruses. Cpf1 genes are associated with the CRISPR locus, coding for an endonuclease that use a guide RNA to find and cleave viral DNA.[1] Cpf1 is a smaller and simpler endonuclease than Cas9, overcoming some of the CRISPR/Cas9 system limitations. CRISPR/Cpf1 could have multiple applications, including treatment of genetic illnesses and degenerative conditions.[2]

Description

Discovery

CRISPR/Cpf1 was found by searching a published database of bacterial genetic sequences for promising bits of DNA. Its identification through bioinformatics as a CRISPR system protein, its naming, and a hidden Markov model (HMM) for its detection were provided in 2012 in a release of the TIGRFAMs database of protein families. Cpf1 appears in many bacterial species. The ultimate Cpf1 endonuclease that was developed into a tool for genome editing was taken from one of the first 16 species known to harbor it.[3] Two candidate enzymes from Acidaminococcus and Lachnospiraceae display efficient genome-editing activity in human cells.[2]

A smaller version of Cas9 from the bacterium Staphylococcus aureus is a potential alternative to Cpf1.[3]

Classification

CRISPR-Cas systems are separated into two classes. Class 1 uses several Cas proteins together with the CRISPR RNAs (crRNA) to build a functional endonuclease. Class 2 CRISPR systems use a single Cas protein with a crRNA. Cpf1 has been recently identified as a Class II, Type V CRISPR/Cas systems containing a 1,300 amino acid protein.[4]

Structure

The Cpf1 locus contains a mixed alpha/beta domain, a RuvC-I followed by a helical region, a RuvC-II and a zinc finger-like domain.[5] The Cpf1 protein has a RuvC-like endonuclease domain that is similar to the RuvC domain of Cas9. Furthermore, Cpf1 does not have a HNH endonuclease domain, and the N-terminal of Cpf1 does not have the alpha-helical recognition lobe of Cas9.[4]

Cpf1 CRISPR-Cas domain architecture shows that Cpf1 is functionally unique, being classified as Class 2, type V CRISPR system. The Cpf1 loci encode Cas1, Cas2 and Cas4 proteins more similar to types I and III than from type II systems. Database searches suggest the abundance of Cpf1-family proteins in many bacterial species.[4]

Functional Cpf1 doesn’t need the tracrRNA, therefore, only crRNA is required. This benefits genome editing because Cpf1 is not only smaller than Cas9, but also it has a smaller sgRNA molecule (proximately half as many nucleotides as Cas9).[6]

The Cpf1-crRNA complex cleaves target DNA or RNA by identification of a protospacer adjacent motif 5'-YTN-3'[7] (where "Y" is a pyrimidine[8] and "N" is any nucleobase) , in contrast to the G-rich PAM targeted by Cas9. After identification of PAM, Cpf1 introduces a sticky-end-like DNA double- stranded break of 4 or 5 nucleotides overhang.[5]

Mechanism

The CRISPR/Cpf1 system consist of a Cpf1 enzyme and a guide RNA that finds and positions the complex at the correct spot on the double helix to cleave target DNA. CRISPR/Cpf1 systems activity has three stages:[3]

  • Adaptation: Cas1 and Cas2 proteins facilitate the adaptation of small fragments of DNA into the CRISPR array. .
  • Formation of crRNAs: processing of pre-cr-RNAs producing of mature crRNAs to guide the Cas protein.
  • Interference: the Cpf1 is bound to a crRNA to form a binary complex to identify and cleave a target DNA sequence.

Cas9 vs. Cpf1

Cas9 requires two RNA molecules to cut DNA while Cpf1 needs one. The proteins also cut DNA at different places, offering researchers more options when selecting an editing site. Cas9 cuts both strands in a DNA molecule at the same position, leaving behind blunt ends. Cpf1 leaves one strand longer than the other, creating sticky ends. The sticky ends aid in the incorporation of new sequences of DNA, making Cpf1 more efficient at gene introductions than Cas9.[3] Although the CRISPR/Cas9 system can efficiently disable genes, it is challenging to insert genes or generate a knock-in.[1] Cpf1 lacks tracrRNA, utilizes a T-rich PAM and cleaves DNA via a staggered DNA DSB.[6]

In summary, important differences between Cpf1 and Cas9 systems are that Cpf1:[9]

  • Recognizes different PAMs, enabling new targeting possibilities.
  • Creates 4-5 nt long sticky ends, instead of blunt ends produced by Cas9, enhancing the efficiency of genetic insertions and specificity during NHEJ or HDR.
  • Cuts target DNA further away from PAM, further away from the Cas9 cutting site, enabling new possibilities for cleaving the DNA.
FeatureCas9Cpf1
StructureTwo RNA required (Or 1 fusion transcript (crRNA+tracrRNA=gRNA)One RNA required
Cutting mechanismBlunt end cutsStaggered end cuts
Cutting siteProximal to recognition siteDistal from recognition site
Target sitesG-rich PAMT-rich PAM

Tools

Multiple aspects influence target efficiency and specificity when using CRISPR, including guide RNA design. Many design models for guide RNA have been suggested, with tools to facilitate optimized design. These include SgRNA designer, CRISPR MultiTargeter, SSFinder.[10]

Intellectual property

CRISPR/Cas9 is subject to Intellectual property disputes while CRISPR/Cpf1 does not have the same issues.[2]

gollark: Don't kiss it. It never helps.
gollark: Ah, the old princess frog...
gollark: Plus many, many other small changes over the millenia.
gollark: Replayability of halloween thing.
gollark: Making it automatic is more effort than ignoring it!

References
  1. "CRISPR-Based Genetic Engineering Gets a Kick in the Cas". Meta Science News. 2015-09-29. Archived from the original on 2017-10-22. Retrieved 2016-05-03.
  2. "Even CRISPR". The Economist. ISSN 0013-0613. Retrieved 2016-05-03.
  3. Ledford, Heidi (2015). "Alternative CRISPR system could improve genome editing". Nature. 526 (7571): 17. doi:10.1038/nature.2015.18432. PMID 26432219.
  4. Makarova, Kira S., et al. "An updated evolutionary classification of CRISPR-Cas systems." Nature Reviews Microbiology (2015).
  5. Zetsche, Bernd; Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Slaymaker, Ian M.; Makarova, Kira S.; Essletzbichler, Patrick; Volz, Sara E.; Joung, Julia; van der Oost, John; Regev, Aviv; Koonin, Eugene V.; Zhang, Feng (October 2015). "Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System". Cell. 163 (3): 759–771. doi:10.1016/j.cell.2015.09.038. PMC 4638220. PMID 26422227.
  6. "Cpf1 Moves in on Cas9 for Next-Gen CRISPR Genome Editing". epigenie.com. Retrieved 2016-05-03.
  7. Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E (2016). "The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA". Nature. 532 (7600): 517–521. doi:10.1038/nature17945. PMID 27096362.
  8. "Nucleotide Codes, Amino Acid Codes, and Genetic Codes". KEGG: Kyoto Encyclopedia of Genes and Genomes. July 15, 2014. Retrieved 2016-05-25.
  9. Yamano, T.; Nishimasu, H.; Zetsche, B.; Hirano, H.; Slaymaker, I. M.; Li, Y.; Fedorova, I.; Nakane, T.; Makarova, K. S.; Koonin, E. V.; et al. (2016). "Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA". Cell. 165 (4): 949–962. doi:10.1016/j.cell.2016.04.003. PMC 4899970. PMID 27114038.
  10. Graham, Daniel B.; Root, David E. (2015-01-01). "Resources for the design of CRISPR gene editing experiments". Genome Biology. 16: 260. doi:10.1186/s13059-015-0823-x. ISSN 1474-760X. PMC 4661947. PMID 26612492.
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