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      Engineering of CRISPR-Cas12b for human genome editing

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          Abstract

          The type-V CRISPR effector Cas12b (formerly known as C2c1) has been challenging to develop for genome editing in human cells, at least in part due to the high temperature requirement of the characterized family members. Here we explore the diversity of the Cas12b family and identify a promising candidate for human gene editing from Bacillus hisashii, BhCas12b. However, at 37 °C, wild-type BhCas12b preferentially nicks the non-target DNA strand instead of forming a double strand break, leading to lower editing efficiency. Using a combination of approaches, we identify gain-of-function mutations for BhCas12b that overcome this limitation. Mutant BhCas12b facilitates robust genome editing in human cell lines and ex vivo in primary human T cells, and exhibits greater specificity compared to S. pyogenes Cas9. This work establishes a third RNA-guided nuclease platform, in addition to Cas9 and Cpf1/Cas12a, for genome editing in human cells.

          Abstract

          The Cas12b family of CRISPR nucleases has been underutilized in mammalian cells due to the high temperature requirement of known members. Here the authors engineer BhCas12b to overcome this limitation for robust and specific genome editing applications in human cells.

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          Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin.

          Numerous prokaryote genomes contain structures known as clustered regularly interspaced short palindromic repeats (CRISPRs), composed of 25-50 bp repeats separated by unique sequence spacers of similar length. CRISPR structures are found in the vicinity of four genes named cas1 to cas4. In silico analysis revealed another cluster of three genes associated with CRISPR structures in many bacterial species, named here as cas1B, cas5 and cas6, and also revealed a certain number of spacers that have homology with extant genes, most frequently derived from phages, but also derived from other extrachromosomal elements. Sequence analysis of CRISPR structures from 24 strains of Streptococcus thermophilus and Streptococcus vestibularis confirmed the homology of spacers with extrachromosomal elements. Phage sensitivity of S. thermophilus strains appears to be correlated with the number of spacers in the CRISPR locus the strain carries. The authors suggest that the spacer elements are the traces of past invasions by extrachromosomal elements, and hypothesize that they provide the cell immunity against phage infection, and more generally foreign DNA expression, by coding an anti-sense RNA. The presence of gene fragments in CRISPR structures and the nuclease motifs in cas genes of both cluster types suggests that CRISPR formation involves a DNA degradation step.
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            Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.

            Microbial CRISPR-Cas systems are divided into Class 1, with multisubunit effector complexes, and Class 2, with single protein effectors. Currently, only two Class 2 effectors, Cas9 and Cpf1, are known. We describe here three distinct Class 2 CRISPR-Cas systems. The effectors of two of the identified systems, C2c1 and C2c3, contain RuvC-like endonuclease domains distantly related to Cpf1. The third system, C2c2, contains an effector with two predicted HEPN RNase domains. Whereas production of mature CRISPR RNA (crRNA) by C2c1 depends on tracrRNA, C2c2 crRNA maturation is tracrRNA independent. We found that C2c1 systems can mediate DNA interference in a 5'-PAM-dependent fashion analogous to Cpf1. However, unlike Cpf1, which is a single-RNA-guided nuclease, C2c1 depends on both crRNA and tracrRNA for DNA cleavage. Finally, comparative analysis indicates that Class 2 CRISPR-Cas systems evolved on multiple occasions through recombination of Class 1 adaptation modules with effector proteins acquired from distinct mobile elements.
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              Diversity and evolution of class 2 CRISPR–Cas systems

              Class 2 CRISPR–Cas systems are characterized by effector modules that consist of a single multidomain protein. In this Analysis, using a computational pipeline, the authors discover three novel families of class 2 effectors that correspond to three new CRISPR–Cas subtypes and present a comprehensive census of class 2 systems that are encoded in complete and draft bacterial and archaeal genomes.
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                Author and article information

                Contributors
                zhang@broadinstitute.org
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                22 January 2019
                22 January 2019
                2019
                : 10
                : 212
                Affiliations
                [1 ]ISNI 0000 0001 2167 1581, GRID grid.413575.1, Howard Hughes Medical Institute, ; Cambridge, USA
                [2 ]GRID grid.66859.34, Broad Institute of MIT and Harvard, ; Cambridge, MA 02142 USA
                [3 ]ISNI 0000 0001 2341 2786, GRID grid.116068.8, McGovern Institute for Brain Research, Department of Biological Engineering, Massachusetts Institute of Technology, ; Cambridge, MA 02139 USA
                [4 ]ISNI 0000 0001 2341 2786, GRID grid.116068.8, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, ; Cambridge, MA 02139 USA
                [5 ]ISNI 0000 0001 2341 2786, GRID grid.116068.8, Department of Biological Engineering, Massachusetts Institute of Technology, ; Cambridge, MA 02139 USA
                [6 ]ISNI 0000 0004 0604 5429, GRID grid.419234.9, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, ; Bethesda, MD 20894 USA
                Author information
                http://orcid.org/0000-0002-5310-7528
                http://orcid.org/0000-0002-3579-0327
                http://orcid.org/0000-0003-3943-8299
                Article
                8224
                10.1038/s41467-018-08224-4
                6342934
                30670702
                3bfe88a7-4eec-4ef2-83d0-d92b46565eff
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 13 November 2018
                : 20 December 2018
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