Cpf1

In molecular biology, CRISPR-associated endonuclease in Prevotella and Francisella 1[lower-alpha 1] or Cpf1 is a single RNA-guided endonuclease lacking a small trans-encoded RNA (a tracrRNA). Instead, Cpf1 uses a T-rich protospacer-adjacent motif (also known as PAM)[4] consisting a of 2-6 base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system[5].[6] It recognizes a T-rich PAM, TTTN, but on the 5' side of the guide. Cpf1 cleaves DNA via a staggered DNA double-stranded break.[7]

Genome editing

Out of 16 Cpf1-family proteins, scientists identified two candidate enzymes from Acidaminococcus and Lachnospiraceae, with efficient genome-editing activity in human cells.[8] Cpf1 was introduced with features that SpCas9 is lacking. Cpf1 requires only a 42-nt short CRISPR RNA (crRNA) to find its target, instead of the ~100-nt guide RNA for SpCas9, and it recognizes a protospacer-adjacent motif (PAM) that is 5′ instead of 3′ of the target site.[9]

Cas9 vs. Cpf1

Feature	Cas9	Cpf1
Structure	Two RNA required (Or 1 fusion transcript (crRNA+tracrRNA=gRNA)	One RNA required
Cutting mechanism	Blunt end cuts	Staggered end cuts
Cutting site	Proximal to recognition site	Distal from recognition site
Target sites	G-rich PAM	T-rich PAM

References

Pollard, T.D. (2007). Cell Biology. Philadelphia: Saunders. pp. 200–203. ISBN 978-1-4160-2255-8.
Latchman DS (Dec 1997). "Transcription factors: an overview". The International Journal of Biochemistry & Cell Biology. 29 (12): 1305–12. doi:10.1016/S1357-2725(97)00085-X. PMC 2002184. PMID 9570129.
Karin M (Feb 1990). "Too many transcription factors: positive and negative interactions". The New Biologist. 2 (2): 126–31. PMID 2128034.
http://www.cell.com/abstract/S0092-8674(15)01200-3 Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
Shah SA, Erdmann S, Mojica FJ, Garrett RA (2013). "Protospacer recognition motifs: mixed identities and functional diversity". RNA Biology. 10 (5): 891–899. doi:10.4161/rna.23764. PMC 3737346. PMID 23403393.
Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F (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.
Using Cpf1 for CRISPR published by "Benchling" (2015)
Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells by Benjamin P Kleinstiver, Shengdar Q Tsai, Michelle S Prew, Nhu T Nguyen, Moira M Welch, Jose M Lopez, Zachary R McCaw, Martin J Aryee & J Keith Joung in "Nature Biotechnology" 34, 869–874 (2016) doi:10.1038/nbt.3620 Published online 27 June 2016
Showdown between Cas9 and Cpf1 by Nature Methods 13, 714 - (2016) doi:10.1038/nmeth.3979 Published online 30 August 2016

- The centromere is the part of a chromosome that links sister chromatids or a dyad. During mitosis, spindle fibers attach to the centromere via the kinetochore.[1]
- A transcription factor or promoter factor is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.[2][3]

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[1] Pollard, T.D. (2007). Cell Biology. Philadelphia: Saunders. pp. 200–203. ISBN 978-1-4160-2255-8.

[pmid9570129-2] Latchman DS (Dec 1997). "Transcription factors: an overview". The International Journal of Biochemistry & Cell Biology. 29 (12): 1305–12. doi:10.1016/S1357-2725(97)00085-X. PMC 2002184. PMID 9570129.

[pmid2128034-3] Karin M (Feb 1990). "Too many transcription factors: positive and negative interactions". The New Biologist. 2 (2): 126–31. PMID 2128034.

[5] ttp://www.cell.com/abstract/S0092-8674(15)01200-3 Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

[pmid23403393-6] Shah SA, Erdmann S, Mojica FJ, Garrett RA (2013). "Protospacer recognition motifs: mixed identities and functional diversity". RNA Biology. 10 (5): 891–899. doi:10.4161/rna.23764. PMC 3737346. PMID 23403393.

[7] Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F (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.

[8] Using Cpf1 for CRISPR published by "Benchling" (2015)

[9] Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells by Benjamin P Kleinstiver, Shengdar Q Tsai, Michelle S Prew, Nhu T Nguyen, Moira M Welch, Jose M Lopez, Zachary R McCaw, Martin J Aryee & J Keith Joung in "Nature Biotechnology" 34, 869–874 (2016) doi:10.1038/nbt.3620 Published online 27 June 2016

[10] Showdown between Cas9 and Cpf1 by Nature Methods 13, 714 - (2016) doi:10.1038/nmeth.3979 Published online 30 August 2016

[4] The centromere is the part of a chromosome that links sister chromatids or a dyad. During mitosis, spindle fibers attach to the centromere via the kinetochore.[1]

A transcription factor or promoter factor is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.[2][3]

[11] The centromere is the part of a chromosome that links sister chromatids or a dyad. During mitosis, spindle fibers attach to the centromere via the kinetochore.[1]

[12] A transcription factor or promoter factor is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.[2][3]

Cpf1

Genome editing

Cas9 vs. Cpf1

See also

References