Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish.
Although the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gR...
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doaj-76a40ba2a21e42159f38ad029d06fe1d2020-11-25T01:45:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01128e018252810.1371/journal.pone.0182528Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish.Yunru ChenShiyang ZengRuikun HuXiangxiu WangWeilai HuangJiangfang LiuLuying WangGuifen LiuYing CaoYong ZhangAlthough the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gRNAs is especially important for zebrafish mutant construction. Besides the sequence features, local chromatin structures may have effects on CRISPR/Cas9 efficiency, which remain largely unexplored. In the only related study in zebrafish, nucleosome organization was not found to have an effect on CRISPR/Cas9 efficiency, which is inconsistent with recent studies in vitro and in mammalian cell lines. To understand the effects of local chromatin structure on CRISPR/Cas9 efficiency in zebrafish, we first determined that CRISPR/Cas9 introduced genome editing mainly before the dome stage. Based on this observation, we reanalyzed our published nucleosome organization profiles and generated chromatin accessibility profiles in the 256-cell and dome stages using ATAC-seq technology. Our study demonstrated that chromatin accessibility showed positive correlation with CRISPR/Cas9 efficiency, but we did not observe a clear correlation between nucleosome organization and CRISPR/Cas9 efficiency. We constructed an online database for zebrafish gRNA selection based on local chromatin structure features that could prove beneficial to zebrafish homozygous mutant construction via CRISPR/Cas9.http://europepmc.org/articles/PMC5553855?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yunru Chen Shiyang Zeng Ruikun Hu Xiangxiu Wang Weilai Huang Jiangfang Liu Luying Wang Guifen Liu Ying Cao Yong Zhang |
spellingShingle |
Yunru Chen Shiyang Zeng Ruikun Hu Xiangxiu Wang Weilai Huang Jiangfang Liu Luying Wang Guifen Liu Ying Cao Yong Zhang Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish. PLoS ONE |
author_facet |
Yunru Chen Shiyang Zeng Ruikun Hu Xiangxiu Wang Weilai Huang Jiangfang Liu Luying Wang Guifen Liu Ying Cao Yong Zhang |
author_sort |
Yunru Chen |
title |
Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish. |
title_short |
Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish. |
title_full |
Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish. |
title_fullStr |
Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish. |
title_full_unstemmed |
Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish. |
title_sort |
using local chromatin structure to improve crispr/cas9 efficiency in zebrafish. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2017-01-01 |
description |
Although the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gRNAs is especially important for zebrafish mutant construction. Besides the sequence features, local chromatin structures may have effects on CRISPR/Cas9 efficiency, which remain largely unexplored. In the only related study in zebrafish, nucleosome organization was not found to have an effect on CRISPR/Cas9 efficiency, which is inconsistent with recent studies in vitro and in mammalian cell lines. To understand the effects of local chromatin structure on CRISPR/Cas9 efficiency in zebrafish, we first determined that CRISPR/Cas9 introduced genome editing mainly before the dome stage. Based on this observation, we reanalyzed our published nucleosome organization profiles and generated chromatin accessibility profiles in the 256-cell and dome stages using ATAC-seq technology. Our study demonstrated that chromatin accessibility showed positive correlation with CRISPR/Cas9 efficiency, but we did not observe a clear correlation between nucleosome organization and CRISPR/Cas9 efficiency. We constructed an online database for zebrafish gRNA selection based on local chromatin structure features that could prove beneficial to zebrafish homozygous mutant construction via CRISPR/Cas9. |
url |
http://europepmc.org/articles/PMC5553855?pdf=render |
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