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      Programmable deletion, replacement, integration, and inversion of large DNA sequences with twin prime editing

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          Abstract

          The targeted deletion, replacement, integration, or inversion of genomic sequences could be used to study or treat human genetic diseases, but existing methods typically require double-strand DNA breaks (DSBs) that lead to undesired consequences including uncontrolled indel mixtures and chromosomal abnormalities. Here, we describe twin prime editing (twinPE), a DSB-independent method that uses a prime editor (PE) protein and two prime editing guide RNAs (pegRNAs) for the programmable replacement or excision of DNA sequences at endogenous human genomic sites. The two pegRNAs template the synthesis of complementary DNA flaps on opposing strands of genomic DNA, which replace the endogenous DNA sequence between the PE-induced nick sites. When combined with a site-specific serine recombinase, twinPE enabled targeted integration of gene-sized DNA plasmids (>5,000 bp) and targeted sequence inversions of 40 kb in human cells. TwinPE expands the capabilities of precision gene editing and may synergize with other tools for the correction or complementation of large or complex human pathogenic alleles.

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          Most cited references56

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          Is Open Access

          A global reference for human genetic variation

          The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
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            A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

            Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
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              Multiplex genome engineering using CRISPR/Cas systems.

              Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.
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                Author and article information

                Journal
                9604648
                20305
                Nat Biotechnol
                Nat Biotechnol
                Nature biotechnology
                1087-0156
                1546-1696
                3 December 2021
                May 2022
                09 December 2021
                09 June 2022
                : 40
                : 5
                : 731-740
                Affiliations
                [1 ]Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
                [2 ]Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
                [3 ]Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
                Author notes
                []Correspondence should be addressed to David R. Liu: drliu@ 123456fas.harvard.edu
                [*]

                These authors contributed equally

                Author contributions

                A.V.A., X.D.G., C.J.P., A.T.N., and J.M.L. designed experiments. A.V.A., X.D.G., C.J.P., A.T.N., L.W.K., A.R., and J.A.M.M. performed experiments and analyzed data. A.V.A., X.D.G., C.J.P. and D.R.L. wrote the manuscript. D.R.L. supervised the research.

                Article
                NIHMS1750706
                10.1038/s41587-021-01133-w
                9117393
                34887556
                e0e6b129-861c-479f-8451-1e93fdc2680f

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