title: Diversity and evolution of class 2 CRISPR-Cas systems.
abstract: Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas.
authors.affiliation: Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia.|National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Shmakov
authors.affiliation: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
authors.forename: Aaron
authors.initials: A
authors.lastname: Smargon
authors.affiliation: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: David
authors.initials: D
authors.lastname: Scott
authors.affiliation: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: David
authors.initials: D
authors.lastname: Cox
authors.affiliation: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
authors.forename: Neena
authors.initials: N
authors.lastname: Pyzocha
authors.affiliation: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Winston
authors.initials: W
authors.lastname: Yan
authors.affiliation: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
authors.forename: Omar O
authors.initials: OO
authors.lastname: Abudayyeh
authors.affiliation: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.|McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
authors.forename: Jonathan S
authors.initials: JS
authors.lastname: Gootenberg
authors.affiliation: National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.affiliation: National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
authors.forename: Yuri I
authors.initials: YI
authors.lastname: Wolf
authors.affiliation: Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia.|Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.|Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Severinov
authors.affiliation: Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.|Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.|McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.|Department of Brain and Cognitive Science, Massachusetts Institute of Technology Cambridge (MIT), Massachusetts 02139, USA.|Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.affiliation: National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D064130:CRISPR-Associated Proteins / Q000235:genetics*; D064113:CRISPR-Cas Systems / Q000235:genetics*; D000072669:Gene Editing / Q000379:methods*; D020745:Genome, Archaeal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D000072417:Protein Domains / Q000235:genetics*
chemical_list: D064130:CRISPR-Associated Proteins