Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining

Published on May 1, 2015in Nature Biotechnology 35.72
· DOI :10.1038/nbt.3190
Takeshi Maruyama14
Estimated H-index: 14
(Massachusetts Institute of Technology),
Stephanie K. Dougan24
Estimated H-index: 24
(Massachusetts Institute of Technology)
+ 3 AuthorsHidde L. Ploegh113
Estimated H-index: 113
(Massachusetts Institute of Technology)
Abstract
The efficiency of homologous recombination-based Cas9 genome editing is increased by inhibiting non-homologous end joining.
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  • Citations (430)
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References31
Published on Mar 1, 2008in Nature Cell Biology 19.06
John C. Christianson14
Estimated H-index: 14
(Stanford University),
Thomas A. Shaler17
Estimated H-index: 17
(Pharmaceutical Product Development)
+ 1 AuthorsRon R. Kopito59
Estimated H-index: 59
(Stanford University)
OS-9 and GRP94 deliver mutant α1-antitrypsin to the Hrd1–SEL1L ubiquitin ligase complex for ERAD
330 Citations Source Cite
Published on Nov 1, 1998in Nature 41.58
Karen M. Frank24
Estimated H-index: 24
(Harvard University),
Jo Ann M. Sekiguchi22
Estimated H-index: 22
(Harvard University)
+ 6 AuthorsFrederick W. Alt154
Estimated H-index: 154
(Harvard University)
Late embryonic lethality and impaired V ( D ) J recombination in mice lacking DNA ligase IV
457 Citations Source Cite
Published on Dec 1, 2012in Nature Cell Biology 19.06
Yuval Rinkevich12
Estimated H-index: 12
,
Taisuke Mori1
Estimated H-index: 1
+ 3 AuthorsIrving L. Weissman173
Estimated H-index: 173
Rinkevich, Weissman and colleagues show that mesothelin-expressing cells from the mesothelium, an epithelial monolayer covering vertebrate cavities and internal organs, generate the fibroblasts and smooth muscle cells (FSMCs) essential for the development of internal organs. Using a genetic lineage tracing approach, they find that these cells participate in generating FSMCs and vasculature, with minimal contributions from neural crest or circulating cells.
73 Citations Source Cite
Published on Jun 13, 2014in Journal of Biological Chemistry 4.01
Clarissa C. Lee4
Estimated H-index: 4
(Massachusetts Institute of Technology),
Elizaveta Freinkman20
Estimated H-index: 20
(Massachusetts Institute of Technology)
+ 1 AuthorsHidde L. Ploegh113
Estimated H-index: 113
(Massachusetts Institute of Technology)
Leucine-rich repeat-containing 8 (LRRC8) proteins have been identified as putative receptors involved in lymphocyte development and adipocyte differentiation. They remain poorly characterized, and no specific function has been assigned to them. There is no consensus on how this family of proteins might function because homology searches suggest that members of the LRRC8 family act not as plasma membrane receptors, but rather as channels that mediate cell-cell signaling. Here we provide experimen...
28 Citations Source Cite
Published on Jan 3, 2014in Science 41.06
Timothy C. Wang63
Estimated H-index: 63
,
Jenny J. Wei2
Estimated H-index: 2
(Massachusetts Institute of Technology)
+ 1 AuthorsEric S. Lander240
Estimated H-index: 240
(Massachusetts Institute of Technology)
The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–Cas9 system for genome editing has greatly expanded the toolbox for mammalian genetics, enabling the rapid generation of isogenic cell lines and mice with modified alleles. Here, we describe a pooled, loss-of-function genetic screening approach suitable for both positive and negative selection that uses a genome-scale lentiviral single-guide RNA (sgRNA) library. sgRNA expression cassettes were stably integrated into...
1,229 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 Nov 1, 2014in Genome Biology 13.21
Li Song8
Estimated H-index: 8
(Johns Hopkins University),
Liliana Florea27
Estimated H-index: 27
(Johns Hopkins University),
Ben Langmead18
Estimated H-index: 18
(Johns Hopkins University)
Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input k-mers and the other holding k-mers likely to be correct. As long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, Bloom filter size can be held constant while maintaining near-constant accuracy. Lighter is parallelized, uses no secondary storage, and is both faster and more mem...
78 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 Dec 1, 1992in Cell 31.40
Luc Van Kaer77
Estimated H-index: 77
(Massachusetts Institute of Technology),
Philip G. Ashton-Rickardt7
Estimated H-index: 7
(Massachusetts Institute of Technology)
+ 1 AuthorsSusumu Tonegawa127
Estimated H-index: 127
(Massachusetts Institute of Technology)
Summary The transporter associated with the antigen processing 1 ( TAP1 ) gene encodes a subunit for a transporter, presumed to be involved in the delivery of peptides across the endoplasmic reticulum membrane to class I molecules. We have generated mice with a disrupted TAP1 gene using embryonic stem cell technology. TAP1-deficient mice are defective in the stable assembly and intracellular transport of class I molecules and consequently show severely reduced levels of surface class I molecules...
591 Citations Source Cite
Published on Dec 15, 2001in Genes & Development 9.46
Andrew J. Pierce20
Estimated H-index: 20
(Cornell University),
Peng Hu2
Estimated H-index: 2
(Cornell University)
+ 2 AuthorsMaria Jasin77
Estimated H-index: 77
(Cornell University)
Chromosomal double-strand breaks (DSBs) in mammalian cells are repaired by either homology-directed repair (HDR), using a homologous sequence as a repair template, or nonhomologous end-joining (NHEJ), which often involves sequence alterations at the DSB site. To characterize the interrelationship of these two pathways, we analyzed HDR of a DSB in cells deficient for NHEJ components. We find that the HDR frequency is enhanced in Ku70−/−, XRCC4−/−, and DNA-PKcs−/− cells, with the increase being pa...
391 Citations Source Cite
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Cited By430
Published on Oct 16, 2015in ACS Synthetic Biology 5.32
Guoqiang Zhang7
Estimated H-index: 7
(Chinese Academy of Sciences),
Yuping Lin10
Estimated H-index: 10
(Chinese Academy of Sciences)
+ 3 AuthorsYanhe Ma38
Estimated H-index: 38
(Chinese Academy of Sciences)
Genome editing is an important tool for building novel genotypes with a desired phenotype. However, the fundamental challenge is to rapidly generate desired alterations on a genome-wide scale. Here, we report TALENs (transcription activator-like effector nucleases)-assisted multiplex editing (TAME), based on the interaction of designed TALENs with the DNA sequences between the critical TATA and GC boxes, for generating multiple targeted genomic modifications. Through iterative cycles of TAME to ...
7 Citations Source Cite
Published on Jul 1, 2015in Human Gene Therapy 4.24
Shaohua Yao1
Estimated H-index: 1
(Sichuan University),
Zhiyao He1
Estimated H-index: 1
(Sichuan University),
Chong Chen17
Estimated H-index: 17
(Sichuan University)
Advances in engineered recombinant nuclease have provided facile and reliable methods for genome editing. Especially with the development of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein-9 nuclease) system, the discovery of various versions of Cas9 proteins and delivery carriers, it is now practicable to introduce desired mutations into the genome, to correct disease-related mutations, and to activate or suppress genes of interest. Epigene...
17 Citations Source Cite
Published on Feb 1, 2016in Journal of Molecular Biology 4.89
Srinivasan Chandrasegaran29
Estimated H-index: 29
(Johns Hopkins University),
Dana Carroll39
Estimated H-index: 39
(University of Utah)
Abstract Genome engineering with programmable nucleases depends on cellular responses to a targeted double-strand break (DSB). The first truly targetable reagents were the zinc finger nucleases (ZFNs) showing that arbitrary DNA sequences could be addressed for cleavage by protein engineering, ushering in the breakthrough in genome manipulation. ZFNs resulted from basic research on zinc finger proteins and the FokI restriction enzyme (which revealed a bipartite structure with a separable DNA-bind...
59 Citations Source Cite
Published on Jul 31, 2015in International Journal of Molecular Sciences 3.69
Mohube Betty Maepa2
Estimated H-index: 2
,
Ilke Roelofse2
Estimated H-index: 2
+ 1 AuthorsPatrick Arbuthnot28
Estimated H-index: 28
Despite the availability of an effective vaccine against hepatitis B virus (HBV), chronic infection with the virus remains a major global health concern. Current drugs against HBV infection are limited by emergence of resistance and rarely achieve complete viral clearance. This has prompted vigorous research on developing better drugs against chronic HBV infection. Advances in understanding the life cycle of HBV and improvements in gene-disabling technologies have been impressive. This has led t...
12 Citations Source Cite
Published on Oct 29, 2015in Swiss Medical Weekly 1.93
Lech Kaczmarczyk2
Estimated H-index: 2
,
Walker S. Jackson10
Estimated H-index: 10
The humble house mouse has long been a workhorse model system in biomedical research. The technology for introducing site-specific genome modifications led to Nobel Prizes for its pioneers and opened a new era of mouse genetics. However, this technology was very time-consuming and technically demanding. As a result, many investigators continued to employ easier genome manipulation methods, though resulting models can suffer from overlooked or underestimated consequences. Another breakthrough, in...
4 Citations Source Cite
Published on Jan 1, 2016in Protein & Cell 6.23
Jeantine E. Lunshof16
Estimated H-index: 16
The mere idea of altering the human germ line has caused excitement as well as fears since decades. The good and, in particular, the dubious motives for such interventions and the anticipated troublesome outcomes have been a recurring theme in literature, art, movies. Until recently, these were merely science fiction scenarios. Yet, considerations about the impact of potential future alteration of the human germ line played a prominent role already in debates ahead of the first clinical trials w...
6 Citations Source Cite
Published on Nov 1, 2015in Stem cell reports 6.54
Mandana Arbab4
Estimated H-index: 4
(Utrecht University),
Sharanya Srinivasan5
Estimated H-index: 5
(Massachusetts Institute of Technology)
+ 2 AuthorsRichard I. Sherwood19
Estimated H-index: 19
(Brigham and Women's Hospital)
We present self-cloning CRISPR/Cas9 (scCRISPR), a technology that allows for CRISPR/Cas9-mediated genomic mutation and site-specific knockin transgene creation within several hours by circumventing the need to clone a site-specific single-guide RNA (sgRNA) or knockin homology construct for each target locus. We introduce a self-cleaving palindromic sgRNA plasmid and a short double-stranded DNA sequence encoding the desired locus-specific sgRNA into target cells, allowing them to produce a locus-...
14 Citations Source Cite
Published on Sep 30, 2015in Molecules and Cells 3.08
Hong Jo Lee6
Estimated H-index: 6
(Seoul National University),
Hyung Chul Lee9
Estimated H-index: 9
(University College London),
Jae Yong Han9
Estimated H-index: 9
(Seoul National University)
Production of genome-edited animals using germline-competent cells and genetic modification tools has provided opportunities for investigation of biological mechanisms in various organisms. The recently reported programmed genome editing technology that can induce gene modification at a target locus in an efficient and precise manner facilitates establishment of animal models. In this regard, the demand for genome-edited avian species, which are some of the most suitable model animals due to the...
9 Citations Source Cite
Published on Jan 1, 2016in Current Issues in Molecular Biology 2.27
Muhammad Jamal10
Estimated H-index: 10
,
Faheem Ahmed Khan10
Estimated H-index: 10
+ 3 AuthorsGang Cao3
Estimated H-index: 3
CRISPR/Cas, a microbial adaptive immune system, has recently been reshaped as a versatile genome editing approach, endowing genome engineering with high efficiency and robustness. The DNA endonuclease Cas, a component of CRISPR system, is directed to specific target within genomes by guide RNA (gRNA) and performs gene editing function. However, the system is still in its infancy and facing enormous challenges such as off-target mutation. Lots of attempts have been made to overcome such off-targe...
13 Citations
Published on Dec 1, 2015in Genome Medicine 8.90
Francis Robert21
Estimated H-index: 21
(McGill University),
Mathilde Barbeau1
Estimated H-index: 1
(McGill University)
+ 2 AuthorsJerry Pelletier71
Estimated H-index: 71
(McGill University)
Background The ability to modify the genome of any cell at a precise location has drastically improved with the recent discovery and implementation of CRISPR/Cas9 editing technology. However, the capacity to introduce specific directed changes at given loci is hampered by the fact that the major cellular repair pathway that occurs following Cas9-mediated DNA cleavage is the erroneous non-homologous end joining (NHEJ) pathway. Homology-directed recombination (HDR) is far less efficient than NHEJ ...
56 Citations Source Cite