Target-Specific Precision of CRISPR-Mediated Genome Editing.

CRISPR-Associated Protein 9 / genetics CRISPR-Cas Systems Cell Proliferation Chromatin / genetics Chromatin Assembly and Disassembly Clustered Regularly Interspaced Short Palindromic Repeats DNA / genetics Gene Deletion Gene Editing / methods HEK293 Cells Hep G2 Cells High-Throughput Nucleotide Sequencing Humans Mutagenesis, Insertional Nucleotide Motifs RNA, Guide, Kinetoplastida / genetics
CRISPR Cas9 chromatin genome editing indel profiles large-scale precise precision predictability sgRNA

Journal

Molecular cell
ISSN: 1097-4164
Titre abrégé: Mol Cell
Pays: United States
ID NLM: 9802571

Informations de publication

Date de publication:
21 02 2019
Historique:
received: 30 07 2018
revised: 25 10 2018
accepted: 20 11 2018
pubmed: 18 12 2018
medline: 25 6 2019
entrez: 18 12 2018
Statut: ppublish

Résumé

The CRISPR-Cas9 system has successfully been adapted to edit the genome of various organisms. However, our ability to predict the editing outcome at specific sites is limited. Here, we examined indel profiles at over 1,000 genomic sites in human cells and uncovered general principles guiding CRISPR-mediated DNA editing. We find that precision of DNA editing (i.e., recurrence of a specific indel) varies considerably among sites, with some targets showing one highly preferred indel and others displaying numerous infrequent indels. Editing precision correlates with editing efficiency and a preference for single-nucleotide homologous insertions. Precise targets and editing outcome can be predicted based on simple rules that mainly depend on the fourth nucleotide upstream of the protospacer adjacent motif (PAM). Indel profiles are robust, but they can be influenced by chromatin features. Our findings have important implications for clinical applications of CRISPR technology and reveal general patterns of broken end joining that can provide insights into DNA repair mechanisms.

Identifiants

DOI: 10.1016/j.molcel.2018.11.031 PMID: 30554945 PMC: PMC6395888
pubmed: 30554945
pii: S1097-2765(18)31001-3
doi: 10.1016/j.molcel.2018.11.031
pmc: PMC6395888
pii:
doi:

Substances chimiques

Chromatin 0
RNA, Guide 0
DNA 9007-49-2
CRISPR-Associated Protein 9 EC 3.1.-

Types de publication

Comparative Study Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

699-713.e6

Subventions

Organisme : Wellcome Trust
ID : FC001152
Pays : United Kingdom
Organisme : Cancer Research UK
ID : FC001110
Pays : United Kingdom
Organisme : Wellcome Trust
ID : FC001110
Pays : United Kingdom
Organisme : Cancer Research UK
ID : FC001152
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom

Informations de copyright

Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

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Auteurs

Anob M Chakrabarti (AM)

Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.

Tristan Henser-Brownhill (T)

Cancer Epigenetics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.

Josep Monserrat (J)

Cancer Epigenetics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.

Anna R Poetsch (AR)

Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan. Electronic address: arpoetsch@gmail.com.

Nicholas M Luscombe (NM)

Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan.

Paola Scaffidi (P)

Cancer Epigenetics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Cancer Institute, University College London, London WC1E 6DD, UK. Electronic address: paola.scaffidi@crick.ac.uk.

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Classifications MeSH

Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines associées aux CRISPR › Protéine-9 associée à CRISPR › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Phénomènes génétiques › Régulation de l'expression des gènes › Épigenèse génétique › Extinction de l'expression des gènes › Systèmes CRISPR-Cas › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Phénomènes physiologiques › Croissance et développement › Croissance › Processus de croissance cellulaire › Prolifération cellulaire › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Structures de chromosome › Chromatine › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Phénomènes génétiques › Régulation de l'expression des gènes › Assemblage et désassemblage de la chromatine › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées en tandem › Clustered regularly interspaced short palindromic repeats › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Phénomènes génétiques › Mutagenèse › Délétion de séquence › Délétion de gène › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Techniques d'investigation › Techniques génétiques › Génie génétique › Édition de gène › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Cellules › Cellules épithéliales › Cellules HEK293 › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Cellules › Cellules épithéliales › Hépatocytes › Cellules HepG2 › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Phénomènes génétiques › Mutagenèse › Mutagenèse par insertion › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Motifs nucléotidiques › Target-Specific Precision of CRISPR-Mediated...
Recherchemedicale.com › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › ARN guide › Target-Specific Precision of CRISPR-Mediated...