Literature DB >> 27494557

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity.

Josh Tycko1, Vic E Myer1, Patrick D Hsu2.   

Abstract

Advances in the development of delivery, repair, and specificity strategies for the CRISPR-Cas9 genome engineering toolbox are helping researchers understand gene function with unprecedented precision and sensitivity. CRISPR-Cas9 also holds enormous therapeutic potential for the treatment of genetic disorders by directly correcting disease-causing mutations. Although the Cas9 protein has been shown to bind and cleave DNA at off-target sites, the field of Cas9 specificity is rapidly progressing, with marked improvements in guide RNA selection, protein and guide engineering, novel enzymes, and off-target detection methods. We review important challenges and breakthroughs in the field as a comprehensive practical guide to interested users of genome editing technologies, highlighting key tools and strategies for optimizing specificity. The genome editing community should now strive to standardize such methods for measuring and reporting off-target activity, while keeping in mind that the goal for specificity should be continued improvement and vigilance.
Copyright © 2016 Elsevier Inc. All rights reserved.

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Year:  2016        PMID: 27494557      PMCID: PMC4976696          DOI: 10.1016/j.molcel.2016.07.004

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  138 in total

1.  Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria.

Authors:  F J Mojica; C Díez-Villaseñor; E Soria; G Juez
Journal:  Mol Microbiol       Date:  2000-04       Impact factor: 3.501

2.  Stimulation of homologous recombination through targeted cleavage by chimeric nucleases.

Authors:  M Bibikova; D Carroll; D J Segal; J K Trautman; J Smith; Y G Kim; S Chandrasegaran
Journal:  Mol Cell Biol       Date:  2001-01       Impact factor: 4.272

3.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

4.  Identification of genes that are associated with DNA repeats in prokaryotes.

Authors:  Ruud Jansen; Jan D A van Embden; Wim Gaastra; Leo M Schouls
Journal:  Mol Microbiol       Date:  2002-03       Impact factor: 3.501

5.  Factors influencing the development of an anti-factor IX (FIX) immune response following administration of adeno-associated virus-FIX.

Authors:  Y Ge; S Powell; M Van Roey; J G McArthur
Journal:  Blood       Date:  2001-06-15       Impact factor: 22.113

6.  Misincorporation by wild-type and mutant T7 RNA polymerases: identification of interactions that reduce misincorporation rates by stabilizing the catalytically incompetent open conformation.

Authors:  J Huang; L G Brieba; R Sousa
Journal:  Biochemistry       Date:  2000-09-26       Impact factor: 3.162

7.  Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements.

Authors:  Francisco J M Mojica; César Díez-Villaseñor; Jesús García-Martínez; Elena Soria
Journal:  J Mol Evol       Date:  2005-02       Impact factor: 2.395

8.  Highly efficient endogenous human gene correction using designed zinc-finger nucleases.

Authors:  Fyodor D Urnov; Jeffrey C Miller; Ya-Li Lee; Christian M Beausejour; Jeremy M Rock; Sheldon Augustus; Andrew C Jamieson; Matthew H Porteus; Philip D Gregory; Michael C Holmes
Journal:  Nature       Date:  2005-04-03       Impact factor: 49.962

9.  CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies.

Authors:  C Pourcel; G Salvignol; G Vergnaud
Journal:  Microbiology (Reading)       Date:  2005-03       Impact factor: 2.777

10.  Release of tumor necrosis factor-alpha from bovine alveolar macrophages stimulated with bovine respiratory viruses and bacterial endotoxins.

Authors:  S E Bienhoff; G K Allen; J N Berg
Journal:  Vet Immunol Immunopathol       Date:  1992-01-31       Impact factor: 2.046

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  95 in total

1.  Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.

Authors:  Matthew C Canver; Maximilian Haeussler; Daniel E Bauer; Stuart H Orkin; Neville E Sanjana; Ophir Shalem; Guo-Cheng Yuan; Feng Zhang; Jean-Paul Concordet; Luca Pinello
Journal:  Nat Protoc       Date:  2018-04-12       Impact factor: 13.491

Review 2.  Delivering the Messenger: Advances in Technologies for Therapeutic mRNA Delivery.

Authors:  Piotr S Kowalski; Arnab Rudra; Lei Miao; Daniel G Anderson
Journal:  Mol Ther       Date:  2019-02-19       Impact factor: 11.454

3.  Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design.

Authors:  Dong Zhang; Travis Hurst; Dongsheng Duan; Shi-Jie Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-15       Impact factor: 11.205

4.  Marker-free coselection for CRISPR-driven genome editing in human cells.

Authors:  Daniel Agudelo; Alexis Duringer; Lusiné Bozoyan; Caroline C Huard; Sophie Carter; Jeremy Loehr; Dafni Synodinou; Mathieu Drouin; Jayme Salsman; Graham Dellaire; Josée Laganière; Yannick Doyon
Journal:  Nat Methods       Date:  2017-04-17       Impact factor: 28.547

5.  CRISPR/Cas9 Gene Drive: Growing Pains for a New Technology.

Authors:  Floyd A Reed
Journal:  Genetics       Date:  2017-03       Impact factor: 4.562

6.  Nucleosomes Selectively Inhibit Cas9 Off-target Activity at a Site Located at the Nucleosome Edge.

Authors:  John M Hinz; Marian F Laughery; John J Wyrick
Journal:  J Biol Chem       Date:  2016-10-18       Impact factor: 5.157

Review 7.  From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering.

Authors:  Rebecca K Delker; Richard S Mann
Journal:  Adv Exp Med Biol       Date:  2017       Impact factor: 2.622

8.  Genetically engineered mouse models for studying radiation biology.

Authors:  Katherine D Castle; Mark Chen; Amy J Wisdom; David G Kirsch
Journal:  Transl Cancer Res       Date:  2017-07       Impact factor: 1.241

9.  Reduced thermal tolerance in a coral carrying CRISPR-induced mutations in the gene for a heat-shock transcription factor.

Authors:  Phillip A Cleves; Amanda I Tinoco; Jacob Bradford; Dimitri Perrin; Line K Bay; John R Pringle
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-09       Impact factor: 11.205

Review 10.  Base editing the mammalian genome.

Authors:  Emma M Schatoff; Maria Paz Zafra; Lukas E Dow
Journal:  Methods       Date:  2019-03-02       Impact factor: 3.608

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