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Exploring C-To-G Base Editing in Rice, Tomato, and Poplar
As a precise genome editing technology, base editing is broadly used in both basic and applied plant research. Cytosine base editors (CBEs) and adenine base editors (ABEs) represent the two commonly used base editor types that mediate C-to-T and A-to-G base transition changes at the target sites, re...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8525388/ https://www.ncbi.nlm.nih.gov/pubmed/34713268 http://dx.doi.org/10.3389/fgeed.2021.756766 |
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author | Sretenovic, Simon Liu, Shishi Li, Gen Cheng, Yanhao Fan, Tingting Xu, Yang Zhou, Jianping Zheng, Xuelian Coleman, Gary Zhang, Yong Qi, Yiping |
author_facet | Sretenovic, Simon Liu, Shishi Li, Gen Cheng, Yanhao Fan, Tingting Xu, Yang Zhou, Jianping Zheng, Xuelian Coleman, Gary Zhang, Yong Qi, Yiping |
author_sort | Sretenovic, Simon |
collection | PubMed |
description | As a precise genome editing technology, base editing is broadly used in both basic and applied plant research. Cytosine base editors (CBEs) and adenine base editors (ABEs) represent the two commonly used base editor types that mediate C-to-T and A-to-G base transition changes at the target sites, respectively. To date, no transversion base editors have been described in plants. Here, we assessed three C-to-G base editors (CGBEs) for targeting sequences with SpCas9’s canonical NGG protospacer adjacent motifs (PAMs) as well as three PAM-less SpRY-based CGBEs for targeting sequences with relaxed PAM requirements. The analyses in rice and tomato protoplasts showed that these CGBEs could make C-to-G conversions at the target sites, and they preferentially edited the C6 position in the 20-nucleotide target sequence. C-to-T edits, insertions and deletions (indels) were major byproducts induced by these CGBEs in the protoplast systems. Further assessment of these CGBEs in stably transformed rice and poplar plants revealed the preference for editing of non-GC sites, and C-to-T edits are major byproducts. Successful C-to-G editing in stably transgenic rice plants was achieved by rXRCC1-based CGBEs with monoallelic editing efficiencies up to 38% in T0 lines. The UNG-rAPOBEC1 (R33A)-based CGBE resulted in successful C-to-G editing in polar, with monoallelic editing efficiencies up to 6.25% in T0 lines. Overall, this study revealed that different CGBEs have different preference on preferred editing sequence context, which could be influenced by cell cycles, DNA repair pathways, and plant species. |
format | Online Article Text |
id | pubmed-8525388 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-85253882021-10-27 Exploring C-To-G Base Editing in Rice, Tomato, and Poplar Sretenovic, Simon Liu, Shishi Li, Gen Cheng, Yanhao Fan, Tingting Xu, Yang Zhou, Jianping Zheng, Xuelian Coleman, Gary Zhang, Yong Qi, Yiping Front Genome Ed Genome Editing As a precise genome editing technology, base editing is broadly used in both basic and applied plant research. Cytosine base editors (CBEs) and adenine base editors (ABEs) represent the two commonly used base editor types that mediate C-to-T and A-to-G base transition changes at the target sites, respectively. To date, no transversion base editors have been described in plants. Here, we assessed three C-to-G base editors (CGBEs) for targeting sequences with SpCas9’s canonical NGG protospacer adjacent motifs (PAMs) as well as three PAM-less SpRY-based CGBEs for targeting sequences with relaxed PAM requirements. The analyses in rice and tomato protoplasts showed that these CGBEs could make C-to-G conversions at the target sites, and they preferentially edited the C6 position in the 20-nucleotide target sequence. C-to-T edits, insertions and deletions (indels) were major byproducts induced by these CGBEs in the protoplast systems. Further assessment of these CGBEs in stably transformed rice and poplar plants revealed the preference for editing of non-GC sites, and C-to-T edits are major byproducts. Successful C-to-G editing in stably transgenic rice plants was achieved by rXRCC1-based CGBEs with monoallelic editing efficiencies up to 38% in T0 lines. The UNG-rAPOBEC1 (R33A)-based CGBE resulted in successful C-to-G editing in polar, with monoallelic editing efficiencies up to 6.25% in T0 lines. Overall, this study revealed that different CGBEs have different preference on preferred editing sequence context, which could be influenced by cell cycles, DNA repair pathways, and plant species. Frontiers Media S.A. 2021-09-15 /pmc/articles/PMC8525388/ /pubmed/34713268 http://dx.doi.org/10.3389/fgeed.2021.756766 Text en Copyright © 2021 Sretenovic, Liu, Li, Cheng, Fan, Xu, Zhou, Zheng, Coleman, Zhang and Qi. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genome Editing Sretenovic, Simon Liu, Shishi Li, Gen Cheng, Yanhao Fan, Tingting Xu, Yang Zhou, Jianping Zheng, Xuelian Coleman, Gary Zhang, Yong Qi, Yiping Exploring C-To-G Base Editing in Rice, Tomato, and Poplar |
title | Exploring C-To-G Base Editing in Rice, Tomato, and Poplar |
title_full | Exploring C-To-G Base Editing in Rice, Tomato, and Poplar |
title_fullStr | Exploring C-To-G Base Editing in Rice, Tomato, and Poplar |
title_full_unstemmed | Exploring C-To-G Base Editing in Rice, Tomato, and Poplar |
title_short | Exploring C-To-G Base Editing in Rice, Tomato, and Poplar |
title_sort | exploring c-to-g base editing in rice, tomato, and poplar |
topic | Genome Editing |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8525388/ https://www.ncbi.nlm.nih.gov/pubmed/34713268 http://dx.doi.org/10.3389/fgeed.2021.756766 |
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