CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes
Adler, Benjamin A ; Trinidad, Marena I ; Bellieny-Rabelo, Daniel ; Zhang, Elaine ; Karp, Hannah M ; Skopintsev, Petr ; Thornton, Brittney W ; Weissman, Rachel F ; Yoon, Peter H ; Chen, LinXing ... show 10 more
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Trinidad, Marena I
Bellieny-Rabelo, Daniel
Zhang, Elaine
Karp, Hannah M
Skopintsev, Petr
Thornton, Brittney W
Weissman, Rachel F
Yoon, Peter H
Chen, LinXing
Hessler, Tomas
Eggers, Amy R
Colognori, David
Boger, Ron
Doherty, Erin E
Tsuchida, Connor A
Tran, Ryan V
Hofman, Laura
Shi, Honglue
Wasko, Kevin M
Zhou, Zehan
Xia, Chenglong
Al-Shimary, Muntathar J
Patel, Jaymin R
Thomas, Vienna C J X
Pattali, Rithu
Kan, Matthew J
Vardapetyan, Anna
Yang, Alana
Lahiri, Arushi
Maxwell, Micaela F
Murdock, Andrew G
Ramit, Glenn C
Henderson, Hope R
Calvert, Roland W
Bamert, Rebecca S
Knott, Gavin J
Lapinaite, Audrone
Pausch, Patrick
Cofsky, Joshua C
Sontheimer, Erik J
Wiedenheft, Blake
Fineran, Peter C
Brouns, Stan J J
Sashital, Dipali G
Thomas, Brian C
Brown, Christopher T
Goltsman, Daniela S A
Barrangou, Rodolphe
Siksnys, Virginius
Banfield, Jillian F
Savage, David F
Doudna, Jennifer A
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UMass Chan Affiliations
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Abstract
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.
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Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon PH, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, Tsuchida CA, Tran RV, Hofman L, Shi H, Wasko KM, Zhou Z, Xia C, Al-Shimary MJ, Patel JR, Thomas VCJX, Pattali R, Kan MJ, Vardapetyan A, Yang A, Lahiri A, Maxwell MF, Murdock AG, Ramit GC, Henderson HR, Calvert RW, Bamert RS, Knott GJ, Lapinaite A, Pausch P, Cofsky JC, Sontheimer EJ, Wiedenheft B, Fineran PC, Brouns SJJ, Sashital DG, Thomas BC, Brown CT, Goltsman DSA, Barrangou R, Siksnys V, Banfield JF, Savage DF, Doudna JA. CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Res. 2024 Jan 5;52(D1):D590-D596. doi: 10.1093/nar/gkad890. Erratum in: Nucleic Acids Res. 2023 Dec 18;: PMID: 37889041; PMCID: PMC10767948.