Genotyping with CRISPR-Cas-derived RNA-guided endonucleases

Published on Dec 1, 2014in Nature Communications 12.35
· DOI :10.1038/ncomms4157
Jong Min Kim21
Estimated H-index: 21
,
Daesik Kim20
Estimated H-index: 20
+ 1 AuthorsJin-Soo Kim51
Estimated H-index: 51
Abstract
Cas9 RNA-guided engineered nucleases (RGENs) induce site-specific DNA cleavages in cultured cells and organisms and are used widely as genome-editing tools. Here, the authors develop an RGEN-based technology to genotype both RGEN-induced mutations and cancer-associated mutations in human cell lines.
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References31
Published on Mar 1, 2013in Nature Biotechnology 35.72
Woong Y. Hwang5
Estimated H-index: 5
,
Yanfang Fu14
Estimated H-index: 14
+ 6 AuthorsJ. Keith Joung59
Estimated H-index: 59
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems have evolved in bacteria and archaea as a defense mechanism to silence foreign nucleic acids of viruses and plasmids. Recent work has shown that bacterial type II CRISPR systems can be adapted to create guide RNAs (gRNAs) capable of directing site-specific DNA cleavage by the Cas9 nuclease in vitro. Here we show that this system can function in vivo to induce targeted genetic modifications in zebra...
1,571 Citations Source Cite
Published on Jan 1, 2010in Genome Research 10.10
Hyung Joo Lee7
Estimated H-index: 7
,
Eunji Kim11
Estimated H-index: 11
,
Jin-Soo Kim51
Estimated H-index: 51
We present a novel approach for generating targeted deletions of genomic segments in human and other eukaryotic cells using engineered zinc finger nucleases (ZFNs). We found that ZFNs designed to target two different sites in a human chromosome could introduce two concurrent DNA double-strand breaks (DSBs) in the chromosome and give rise to targeted deletions of the genomic segment between the two sites. Using this method in human cells, we were able to delete predetermined genomic DNA segments ...
206 Citations Source Cite
Published on Jan 1, 2011in Nature Methods 26.92
Seokjoong Kim13
Estimated H-index: 13
(Seoul National University),
Mi Jung Lee5
Estimated H-index: 5
(Seoul National University)
+ 2 AuthorsJin-Soo Kim51
Estimated H-index: 51
(Seoul National University)
64 Citations Source Cite
Published on Aug 1, 2013in Nature Biotechnology 35.72
Vladimir Nekrasov14
Estimated H-index: 14
,
Brian J. Staskawicz73
Estimated H-index: 73
+ 2 AuthorsSophien Kamoun83
Estimated H-index: 83
Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease
432 Citations Source Cite
Published on Mar 1, 2013in Nature Biotechnology 35.72
Wenyan Jiang11
Estimated H-index: 11
,
David Bikard17
Estimated H-index: 17
+ 2 AuthorsLuciano A. Marraffini33
Estimated H-index: 33
A CRISPR-Cas system is harnessed to introduce template-driven mutations in S. pneumoniae and E. coli at high efficiency without requiring selectable markers.
1,160 Citations Source Cite
Published on Apr 1, 2013in Cell Research 15.39
Nannan Chang8
Estimated H-index: 8
,
Changhong Sun1
Estimated H-index: 1
+ 5 AuthorsJianzhong Jeff Xi1
Estimated H-index: 1
Recent advances with the type II clustered regularly interspaced short palindromic repeats (CRISPR) system promise an improved approach to genome editing. However, the applicability and efficiency of this system in model organisms, such as zebrafish, are little studied. Here, we report that RNA-guided Cas9 nuclease efficiently facilitates genome editing in both mammalian cells and zebrafish embryos in a simple and robust manner. Over 35% of site- specific somatic mutations were found when specif...
487 Citations Source Cite
Published on Aug 1, 2013in Nature Biotechnology 35.72
Qiwei Shan7
Estimated H-index: 7
,
Yanpeng Wang10
Estimated H-index: 10
(Chinese Academy of Sciences)
+ 8 AuthorsCaixia Gao23
Estimated H-index: 23
(Chinese Academy of Sciences)
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698 Citations Source Cite
Published on Feb 15, 2013in Science 41.06
Prashant Mali28
Estimated H-index: 28
(Harvard University),
Luhan Yang16
Estimated H-index: 16
(Harvard University)
+ 5 AuthorsGeorge M Church G M132
Estimated H-index: 132
(Wyss Institute for Biologically Inspired Engineering)
Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the endogenous AAVS1 locus, we obtained targeting rates of 10 to 25% in 293T cells, 13 to 8% in K562 cells, and 2 to 4% in induced pluripotent stem cel...
4,240 Citations Source Cite
Published on Jun 1, 2005in Nature 41.58
Fyodor D. Urnov42
Estimated H-index: 42
(Sangamo BioSciences),
Jeffrey C. Miller35
Estimated H-index: 35
(Sangamo BioSciences)
+ 7 AuthorsMichael C. Holmes45
Estimated H-index: 45
(Sangamo BioSciences)
Permanent modification of the human genome in vivo is impractical owing to the low frequency of homologous recombination in human cells, a fact that hampers biomedical research and progress towards safe and effective gene therapy. Here we report a general solution using two fundamental biological processes: DNA recognition by C2H2 zinc-finger proteins and homology-directed repair of DNA double-strand breaks. Zinc-finger proteins engineered to recognize a unique chromosomal site can be fused to a...
1,270 Citations Source Cite
Published on Aug 1, 2013in Nature Biotechnology 35.72
Jian-Feng Li15
Estimated H-index: 15
,
Julie E. Norville9
Estimated H-index: 9
+ 5 AuthorsJen Sheen70
Estimated H-index: 70
Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9
576 Citations Source Cite
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  • Citations (57)
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Cited By57
Published on Dec 1, 2015in Nature Communications 12.35
Wenjun Jiang5
Estimated H-index: 5
,
Xuejin Zhao2
Estimated H-index: 2
+ 3 AuthorsTing F. Zhu10
Estimated H-index: 10
The cloning of long DNA segments, especially those containing large gene clusters, is of particular importance to synthetic and chemical biology efforts for engineering organisms. While cloning has been a defining tool in molecular biology, the cloning of long genome segments has been challenging. Here we describe a technique that allows the targeted cloning of near-arbitrary, long bacterial genomic sequences of up to 100 kb to be accomplished in a single step. The target genome segment is excis...
48 Citations Source Cite
Published on Jan 1, 2015in Frontiers in Plant Science 3.68
Mukesh K. Jain64
Estimated H-index: 64
Various abiotic stresses, such as drought, salinity, heat, flooding, ion toxicity and radiation are the major constraints to agricultural production. The understanding of molecular basis of plant response to these environmental conditions has been a major focus of research in the past decades. Several genes/pathways and regulatory networks involved in stress responses have been worked out employing various approaches. Quite a few of these components have been used for engineering abiotic stress ...
24 Citations Source Cite
Published on Nov 1, 2015in Nature Biotechnology 35.72
Je Wook Woo2
Estimated H-index: 2
,
Jung-Eun Kim21
Estimated H-index: 21
+ 7 AuthorsJin-Soo Kim51
Estimated H-index: 51
CRISPR-Cas9 genome editing is achieved in Arabidopsis, tobacco, lettuce and rice without introducing foreign DNA into the plants.
263 Citations Source Cite
Published on Jan 1, 2014in Methods in Enzymology 1.98
Hillel T. Schwartz3
Estimated H-index: 3
(California Institute of Technology),
Paul W. Sternberg86
Estimated H-index: 86
(California Institute of Technology)
Genome modification by CRISPR/Cas offers its users the ability to target endogenous sites in the genome for cleavage and for engineering precise genomic changes using template-directed repair, all with unprecedented ease and flexibility of targeting. As such, CRISPR/Cas is just part of a set of recently developed and rapidly improving tools that offer great potential for researchers to functionally access the genomes of organisms that have not previously been extensively used in a laboratory set...
2 Citations Source Cite
Wenhui Hu26
Estimated H-index: 26
(Temple University),
Rafal M. Kaminski27
Estimated H-index: 27
(Temple University)
+ 9 AuthorsJonathan Karn22
Estimated H-index: 22
(Case Western Reserve University)
AIDS remains incurable due to the permanent integration of HIV-1 into the host genome, imparting risk of viral reactivation even after antiretroviral therapy. New strategies are needed to ablate the viral genome from latently infected cells, because current methods are too inefficient and prone to adverse off-target effects. To eliminate the integrated HIV-1 genome, we used the Cas9/guide RNA (gRNA) system, in single and multiplex configurations. We identified highly specific targets within the ...
267 Citations Source Cite
Published on May 1, 2015in Scientific Reports 4.12
Xiaoxiao Zhu7
Estimated H-index: 7
,
Yajie Xu1
Estimated H-index: 1
+ 11 AuthorsDongdong Fan3
Estimated H-index: 3
The rapid generation of various species and strains of laboratory animals using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, the dominant approach for genotyping of genome-modified animals has been the T7E1 endonuclease cleavage assay. Here, we present a polyacrylamide gel electrophoresis-based (PAGE) method to genotype mice harboring different types of indel mutations. We developed 6 strains of genome-modified mice using CRISPR/Cas9 sys...
84 Citations Source Cite
Published on Dec 1, 2015in Genome Biology 13.21
Tomomi Aida11
Estimated H-index: 11
(Tokyo Medical and Dental University),
Keiho Chiyo1
Estimated H-index: 1
(Tokyo Medical and Dental University)
+ 7 AuthorsKohichi Tanaka49
Estimated H-index: 49
(Tokyo Medical and Dental University)
Although the CRISPR/Cas system has enabled one-step generation of knockout mice, low success rates of cassette knock-in limit its application range. Here we show that cloning-free, direct nuclear delivery of Cas9 protein complex with chemically synthesized dual RNAs enables highly efficient target digestion, leading to generation of knock-in mice carrying a functional cassette with up to 50% efficiency, compared with just 10% by a commonly used method consisting of Cas9 mRNA and single guide RNA...
115 Citations Source Cite
Published on Nov 28, 2014in Science 41.06
Jennifer A. Doudna90
Estimated H-index: 90
(University of California, Berkeley),
Emmanuelle Charpentier28
Estimated H-index: 28
(Hannover Medical School)
The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of...
1,693 Citations Source Cite
Published on Aug 1, 2014in Methods 4.00
Young Hoon Sung11
Estimated H-index: 11
(Yonsei University),
Young Jin3
Estimated H-index: 3
(Yonsei University)
+ 1 AuthorsH.W. Lee34
Estimated H-index: 34
(Yonsei University)
Abstract The use of engineered nucleases in one-cell stage mouse embryos is emerging as an efficient alternative to conventional gene targeting in mouse embryonic stem (ES) cells. These nucleases are designed or reprogrammed to specifically induce double strand breaks (DSBs) at a desired genomic locus, and efficiently introduce mutations by both error-prone and error-free DNA repair mechanisms. Since these mutations frequently result in the loss or alteration of gene function by inserting, delet...
13 Citations Source Cite
Published on Jun 1, 2015in Journal of NeuroVirology 3.23
Kamel Khalili62
Estimated H-index: 62
(Temple University),
Rafal M. Kaminski27
Estimated H-index: 27
(Temple University)
+ 2 AuthorsWenhui Hu26
Estimated H-index: 26
(Temple University)
Current therapy for controlling human immunodeficiency virus (HIV-1) infection and preventing acquired immunodeficiency syndrome (AIDS) progression has profoundly decreased viral replication in cells susceptible to HIV-1 infection, but it does not eliminate the low level of viral replication in latently infected cells, which contain integrated copies of HIV-1 proviral DNA. There is an urgent need for the development of HIV-1 genome eradication strategies that will lead to a permanent or “sterile...
28 Citations Source Cite