Cited by 41CRISPR and Genetic EngineeringRNA regulation and diseasePlant Molecular Biology Research

A cytosine base editor toolkit with varying activity windows and target scopes for versatile gene manipulation in plants

Open access
Xiong, Xiangyu, Li, Zhenxiang, Liang, Jieping, Liu, Kehui, Li, Chenlong, Li, Jian-Feng·2022·Nucleic Acids Research

Abstract

CRISPR/Cas-derived base editing tools empower efficient alteration of genomic cytosines or adenines associated with essential genetic traits in plants and animals. Diversified target sequences and customized editing products call for base editors with distinct features regarding the editing window and target scope. Here we developed a toolkit of plant base editors containing AID10, an engineered human AID cytosine deaminase. When fused to the N-terminus or C-terminus of the conventional Cas9 nickase (nSpCas9), AID10 exhibited a broad or narrow activity window at the protospacer adjacent motif (PAM)-distal and -proximal protospacer, respectively, while AID10 fused to both termini conferred an additive activity window. We further replaced nSpCas9 with orthogonal or PAM-relaxed Cas9 variants to widen target scopes. Moreover, we devised dual base editors with AID10 located adjacently or distally to the adenine deaminase ABE8e, leading to juxtaposed or spaced cytosine and adenine co-editing at the same target sequence in plant cells. Furthermore, we expanded the application of this toolkit in plants for tunable knockdown of protein-coding genes via creating upstream open reading frame and for loss-of-function analysis of non-coding genes, such as microRNA sponges. Collectively, this toolkit increases the functional diversity and versatility of base editors in basic and applied plant research.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/gkac166

Cites

86 of 86 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • These single nucleotide polymorphisms (SNPs) can now be achieved through base or prime editing.

    “These single nucleotide polymorphisms (SNPs) can now be achieved through base or prime editing (Lin et al., 2021;Xiong et al., 2022).”
  • Base editing can be repurposed as a gene loss of function tool by creating a stop codon or a gene knockdown by creating an upstream open reading frame (uORF).

    “It can also be repurposed as a gene loss of function tool by creating a stop codon or a gene knockdown by creating an upstream open reading frame (uORF) (Billon et al., 2017;Kuscu et al., 2017;Xiong et al., 2022).”
  • Base-editing studies conducted in Arabidopsis and rice provide confidence in using this technique in barley to improve useful traits, for instance, inducing early or late flowering to escape stress windows such as those for frost or drought.

    “Base-editing studies conducted in Arabidopsis and rice provide confidence in using this technique in barley to improve useful traits, for instance, inducing early or late flowering to escape stress windows such as those for frost or drought (Li et al., 2020;Xiong et al., 2022).”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Xiong, X., Li, Z., Liang, J., Liu, K., Li, C., & Li, J.-F.
Affiliations
  • Sun Yat-sen University (CN)
  • MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
Corresponding author
Li, Zhenxiang
Venue
Nucleic Acids Research
Published
2022-03-14
Volume
50
Issue
6
Pages
3565-3580
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
OpenAlex
W4214533861
Cited by
41
References
86
Citations by year
2026: 6 · 2025: 5 · 2024: 11 · 2023: 14 · 2022: 5
FWCI
2.85
Type
journal article
Language
en
Open access
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • National Transgenic Science and Technology Major Program of China (2019ZX08010003-001-009)
  • Foundation of Guangzhou Science and Technology Key Project (201904020041)
  • National Natural Science Foundation of China (32125004)
  • China Postdoctoral Science Foundation (2020TQ0387)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
Keywords
cytosine base editing, protospacer adjacent motif, ABE8e, plant genome editing, microRNA sponge
MeSH terms
Gene Editing, CRISPR-Associated Protein 9, Adenine, Animals, Cytosine, CRISPR-Cas Systems

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review