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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...

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Autores principales: Sretenovic, Simon, Liu, Shishi, Li, Gen, Cheng, Yanhao, Fan, Tingting, Xu, Yang, Zhou, Jianping, Zheng, Xuelian, Coleman, Gary, Zhang, Yong, Qi, Yiping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
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.
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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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