Computational Tools and Resources Supporting CRISPR-Cas Experiments.

Base Sequence CRISPR-Cas Systems / genetics Computational Biology / methods DNA Repair / genetics Gene Editing RNA, Guide, Kinetoplastida / genetics
CRISPR HDR NGS analysis NHEJ database genome editing microhomology off-target predictive algorithms sgRNA sgRNA design

Journal

Cells
ISSN: 2073-4409
Titre abrégé: Cells
Pays: Switzerland
ID NLM: 101600052

Informations de publication

Date de publication:
22 05 2020
Historique:
received: 06 05 2020
revised: 18 05 2020
accepted: 20 05 2020
entrez: 28 5 2020
pubmed: 28 5 2020
medline: 26 2 2021
Statut: epublish

Résumé

The CRISPR-Cas system has become a cutting-edge technology that revolutionized genome engineering. The use of Cas9 nuclease is currently the method of choice in most tasks requiring a specific DNA modification. The rapid development in the field of CRISPR-Cas is reflected by the constantly expanding ecosystem of computational tools aimed at facilitating experimental design and result analysis. The first group of CRISPR-Cas-related tools that we review is dedicated to aid in guide RNA design by prediction of their efficiency and specificity. The second, relatively new group of tools exploits the observed biases in repair outcomes to predict the results of CRISPR-Cas edits. The third class of tools is developed to assist in the evaluation of the editing outcomes by analysis of the sequencing data. These utilities are accompanied by relevant repositories and databases. Here we present a comprehensive and updated overview of the currently available CRISPR-Cas-related tools, from the perspective of a user who needs a convenient and reliable means to facilitate genome editing experiments at every step, from the guide RNA design to analysis of editing outcomes. Moreover, we discuss the current limitations and challenges that the field must overcome for further improvement in the CRISPR-Cas endeavor.

Identifiants

DOI: 10.3390/cells9051288 PMID: 32455882 PMC: PMC7290941
pubmed: 32455882
pii: cells9051288
doi: 10.3390/cells9051288
pmc: PMC7290941
pii:
doi:

Substances chimiques

RNA, Guide 0

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

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Auteurs

Pawel Sledzinski (P)

Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
ORCID: 0000-0002-4671-5189

Mateusz Nowaczyk (M)

Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.

Marta Olejniczak (M)

Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
ORCID: 0000-0001-8471-6302

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