Evidence map›Paper›PMID 38616491›Full record

ArticlePlant communications2024

Boosting genome editing in plants with single transcript unit surrogate reporter systems.

Xu Tang, Qiurong Ren, Xiaodan Yan, Rui Zhang, Li Liu, Qinqin Han, Xuelian Zheng, Yiping Qi, Hongyuan Song, Yong Zhang

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Plant communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
2.3field-weighted citation impact, top 12% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed, 10 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. Review
  5. Article
  6. DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025
    Review
  7. Review
  8. Article
  9. Article
  10. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 3 institutions in 2 countries.

Xu TangChongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
Qiurong RenCollege of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; School of Synbiology, School of Life Science, Shanxi University, Taiyuan 030006, China.
Xiaodan YanKey Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China.
Rui ZhangDepartment of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
Li LiuDepartment of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
Qinqin HanDepartment of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
Xuelian ZhengChongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China.
Yiping QiDepartment of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA. Electronic address: yiping@umd.edu.
Hongyuan SongKey Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China. Electronic address: yuahs@swu.edu.cn.
Yong ZhangChongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400715, China; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China; Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China. Electronic address: zhangyong916@swu.edu.cn.
Southwest University · CNUniversity of Electronic Science and Technology of China · CNUniversity of Maryland, College Park · US

Funding

Non-US Government Research Support type
6 · The paper itself

Abstract

CRISPR-Cas-based genome editing holds immense promise for advancing plant genomics and crop enhancement. However, the challenge of low editing activity complicates the identification of editing events. In this study, we introduce multiple single transcript unit surrogate reporter (STU-SR) systems to enhance the selection of genome-edited plants. These systems use the same single guide RNAs designed for endogenous genes to edit reporter genes, establishing a direct link between reporter gene editing activity and that of endogenous genes. Various strategies are used to restore functional reporter genes after genome editing, including efficient single-strand annealing (SSA) for homologous recombination in STU-SR-SSA systems. STU-SR-base editor systems leverage base editing to reinstate the start codon, enriching C-to-T and A-to-G base editing events. Our results showcase the effectiveness of these STU-SR systems in enhancing genome editing events in the monocot rice, encompassing Cas9 nuclease-based targeted mutagenesis, cytosine base editing, and adenine base editing. The systems exhibit compatibility with Cas9 variants, such as the PAM-less SpRY, and are shown to boost genome editing in Brassica oleracea, a dicot vegetable crop. In summary, we have developed highly efficient and versatile STU-SR systems for enrichment of genome-edited plants.

Indexed as

CRISPR-Cas SystemsGene EditingGenome, PlantOryzaGenes, ReporterRNA, Guide, CRISPR-Cas SystemsRNA, Guide, CRISPR-Cas Systemsadenine base editingCRISPR–Cas9cytosine base editingsingle strand annealingsingle transcript unitSRSSASTUsurrogate reporter

Identifiers

PMID38616491
PMCPMC11211634
OpenAlexW4394807944

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.