University of Oulu

Uusi-Mäkelä MIE, Barker HR, Bäuerlein CA, Häkkinen T, Nykter M, Rämet M (2018) Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio). PLoS ONE 13(4): e0196238. https://doi.org/10.1371/journal.pone.0196238

Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio)

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Author: Uusi-Mäkelä, Meri I. E.1; Barker, Harlan R.2; Bäuerlein, Carina A.1;
Organizations: 1Laboratory of Experimental Immunology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere
2Laboratory of Anatomy, Faculty of Medicine and Life Sciences, University of Tampere
3Laboratory of Computational Biology, BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere
4PEDEGO Research Unit, Medical Research Center Oulu, and Department of Children and Adolescents, Oulu University Hospital
5Department of Pediatrics, Tampere University Hospital
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 2.9 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe2018080933579
Language: English
Published: Public Library of Science, 2018
Publish Date: 2018-08-09
Description:

Abstract

CRISPR-Cas9 technology is routinely applied for targeted mutagenesis in model organisms and cell lines. Recent studies indicate that the prokaryotic CRISPR-Cas9 system is affected by eukaryotic chromatin structures. Here, we show that the likelihood of successful mutagenesis correlates with transcript levels during early development in zebrafish (Danio rerio) embryos. In an experimental setting, we found that guide RNAs differ in their onset of mutagenesis activity in vivo. Furthermore, some guide RNAs with high in vitro activity possessed poor mutagenesis activity in vivo, suggesting the presence of factors that limit the mutagenesis in vivo. Using open access datasets generated from early developmental stages of the zebrafish, and guide RNAs selected from the CRISPRz database, we provide further evidence for an association between gene expression during early development and the success of CRISPR-Cas9 mutagenesis in zebrafish embryos. In order to further inspect the effect of chromatin on CRISPR-Cas9 mutagenesis, we analysed the relationship of selected chromatin features on CRISPR-Cas9 mutagenesis efficiency using publicly available data from zebrafish embryos. We found a correlation between chromatin openness and the efficiency of CRISPR-Cas9 mutagenesis. These results indicate that CRISPR-Cas9 mutagenesis is influenced by chromatin accessibility in zebrafish embryos.

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Series: PLoS one
ISSN: 1932-6203
ISSN-E: 1932-6203
ISSN-L: 1932-6203
Volume: 13
Issue: 4
Article number: e0196238
DOI: 10.1371/journal.pone.0196238
OADOI: https://oadoi.org/10.1371/journal.pone.0196238
Type of Publication: A1 Journal article – refereed
Field of Science: 3111 Biomedicine
Subjects:
Funding: This study was supported with the following grants: Tampere Tuberculosis Foundation (http://www.tuberkuloosisaatio.fi/) (MU;MR); Finnish Concordia Fund (http://www.konkordia-liitto.com/) (MU); Sigrid Juselius Foundation (http://sigridjuselius.fi/apurahat/) (MR); University of Tampere Doctoral School (http://www.uta.fi/english/doctoralschool/index.html) (MU); Finnish Cultural Foundation – Maili Autio Fund (https://skr.fi/) (HB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Copyright information: © 2018 Uusi-Mäkelä et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
  https://creativecommons.org/licenses/by/4.0/