☆ 4.7 Review

Prime editing: Mechanism insight and recent applications in plants

PLANT BIOTECHNOLOGY JOURNAL (2024)

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Summary: This study identified factors affecting PE2 efficiency through high-throughput evaluation and developed three computational models to predict pegRNA efficiency, which can be applied to edits of various types and positions. Spearman's correlations between 0.47 and 0.81 were found when testing the accuracy of the predictions using independent test data sets.

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Summary: The study found that DNA mismatch repair (MMR) hinders prime editing and promotes undesired byproducts, but the efficiency of substitution, small insertion, and small deletion edits can be enhanced by developing PE4 and PE5 prime editing systems. Strategic silent mutations near the intended edit and optimization of prime editor protein also contribute to improved editing outcomes.

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Summary: The study systematically evaluated the mismatch tolerance, off-target editing, and genome-wide variants induced by prime editors in plant cells, showing high precision and low off-target effects in plant genome editing.

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Identification of herbicide resistance OsACC1 mutations via in planta prime-editing-library screening in rice

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Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit

Xingang Wang et al.

Summary: The study found that targeted mutations in conserved promoter sequences of the repressor of stem cell proliferation, SlCLV3, have a weak impact on fruit locule number, but pairwise combinations of these mutations mildly enhance this trait, revealing additive and synergistic relationships. Conversely, the positive regulator of stem cell proliferation, SlWUS, is more tolerant to promoter perturbations. The results suggest that complex interactions among cis-regulatory variants can shape quantitative variation in crop traits.

NATURE PLANTS (2021)

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Article Biotechnology & Applied Microbiology

Spelling Changes and Fluorescent Tagging With Prime Editing Vectors for Plants

Li Wang et al.

Summary: Prime editing is an improved version of the CRISPR-Cas system, utilizing a fusion protein and guide RNA to achieve specified substitutions, insertions, and deletions in the target DNA. Recent studies have demonstrated successful Prime editing in rice and wheat, including significant insertions.

FRONTIERS IN GENOME EDITING (2021)

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Article Plant Sciences

Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes

Lei Liu et al.

Summary: By using CRISPR-Cas9 genome editing, weak promoter alleles of CLE genes and a null allele of a partially redundant compensating CLE gene were engineered in maize to increase multiple maize grain-yield-related traits, demonstrating the potential of genomic editing in crop improvement.

NATURE PLANTS (2021)

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Review Biochemistry & Molecular Biology

Transgene Stacking as Effective Tool for Enhanced Disease Resistance in Plants

Kashmala Shehryar et al.

MOLECULAR BIOTECHNOLOGY (2020)

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Review Multidisciplinary Sciences

The promise and challenge of therapeutic genome editing

Jennifer A. Doudna

NATURE (2020)

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Article Biotechnology & Applied Microbiology

Highly efficient homology-directed repair using CRISPR/Cpf1-geminiviral replicon in tomato

Tien Van Vu et al.

PLANT BIOTECHNOLOGY JOURNAL (2020)

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Letter Biotechnology & Applied Microbiology

Engineering herbicide resistance via prime editing in rice

Haroon Butt et al.

PLANT BIOTECHNOLOGY JOURNAL (2020)

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Letter Biotechnology & Applied Microbiology

Precision genome engineering in rice using prime editing system

Kai Hua et al.

PLANT BIOTECHNOLOGY JOURNAL (2020)

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Letter Biochemistry & Molecular Biology

Plant Prime Editors Enable Precise Gene Editing in Rice Cells

Xu Tang et al.

MOLECULAR PLANT (2020)

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Letter Biochemistry & Molecular Biology

Precise Modifications of Both Exogenous and Endogenous Genes in Rice by Prime Editing

Huiyuan Li et al.

MOLECULAR PLANT (2020)

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Letter Biochemistry & Molecular Biology

Versatile Nucleotides Substitution in Plant Using an Improved Prime Editing System

Wen Xu et al.

MOLECULAR PLANT (2020)

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Article Biotechnology & Applied Microbiology

Prime genome editing in rice and wheat

Qiupeng Lin et al.

NATURE BIOTECHNOLOGY (2020)

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Editorial Material Biochemistry & Molecular Biology

Toward Precision Genome Editing in Crop Plants

Jingying Li et al.

MOLECULAR PLANT (2020)

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Review Biotechnology & Applied Microbiology

Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors

Andrew V. Anzalone et al.

NATURE BIOTECHNOLOGY (2020)

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Letter Biotechnology & Applied Microbiology

Quantitative regulation of Waxy expression by CRISPR/Cas9-based promoter and 5'UTR-intron editing improves grain quality in rice

Dongchang Zeng et al.

PLANT BIOTECHNOLOGY JOURNAL (2020)

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Editorial Material Plant Sciences

Prime Editing: Game Changer for Modifying Plant Genomes

Marek Marzec et al.

TRENDS IN PLANT SCIENCE (2020)

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Article Biotechnology & Applied Microbiology

A GRF-GIF chimeric protein improves the regeneration efficiency of transgenic plants

Juan M. Debernardi et al.

NATURE BIOTECHNOLOGY (2020)

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Article Multidisciplinary Sciences

Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering

Carla Schmidt et al.

NATURE COMMUNICATIONS (2020)

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Article Biotechnology & Applied Microbiology

Prime editing efficiently generates W542L and S621I double mutations in two ALS genes in maize

Yuan-Yuan Jiang et al.

GENOME BIOLOGY (2020)

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Article Biotechnology & Applied Microbiology

Fine-tuning sugar content in strawberry

Sinian Xing et al.

GENOME BIOLOGY (2020)

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Article Plant Sciences

CRISPR-Cas9-mediated induction of heritable chromosomal translocations in Arabidopsis

Natalja Beying et al.

NATURE PLANTS (2020)

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Article Biochemistry & Molecular Biology

Development of Plant Prime-Editing Systems for Precise Genome Editing

Rongfang Xu et al.

PLANT COMMUNICATIONS (2020)

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Review Plant Sciences

CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture

Kunling Chen et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 70 (2019)

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Article Multidisciplinary Sciences

Search-and-replace genome editing without double-strand breaks or donor DNA

Andrew V. Anzalone et al.

NATURE (2019)

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Review Agronomy

Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants

Tien Van Vu et al.

RICE (2019)

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Article Genetics & Heredity

Improving CRISPR-Cas9 Genome Editing Efficiency by Fusion with Chromatin-Modulating Peptides

Xiao Ding et al.

CRISPR JOURNAL (2019)

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Article Biotechnology & Applied Microbiology

Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo

Guanwen Liu et al.

GENOME BIOLOGY (2019)

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Article Biotechnology & Applied Microbiology

Chimeric 3' flanking regions strongly enhance gene expression in plants

Andrew G. Diamos et al.

PLANT BIOTECHNOLOGY JOURNAL (2018)

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Review Biochemical Research Methods

Serine Integrases: Advancing Synthetic Biology

Christine A. Merrick et al.

ACS SYNTHETIC BIOLOGY (2018)

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Editorial Material Biotechnology & Applied Microbiology

Genome editing of upstream open reading frames enables translational control in plants

Huawei Zhang et al.

NATURE BIOTECHNOLOGY (2018)

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Article Multidisciplinary Sciences

Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo

Robert M. Yarrington et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

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Article Multidisciplinary Sciences

Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting

Fuqiang Chen et al.

NATURE COMMUNICATIONS (2017)

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Article Virology

Pyramiding resistance-conferring gene sequences in crops

Marc Fuchs

CURRENT OPINION IN VIROLOGY (2017)

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Article Biochemistry & Molecular Biology

Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing

Daniel Rodriguez-Leal et al.

CELL (2017)

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Article Biotechnology & Applied Microbiology

Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA

Christopher D. Richardson et al.

NATURE BIOTECHNOLOGY (2016)

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Article Plant Sciences

Precision Targeted Mutagenesis via Cas9 Paired Nickases in Rice

Masafumi Mikami et al.

PLANT AND CELL PHYSIOLOGY (2016)

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Article Multidisciplinary Sciences

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

Fuguo Jiang et al.

SCIENCE (2016)

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Article Biology

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

Max A. Horlbeck et al.

ELIFE (2016)

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Article Biotechnology & Applied Microbiology

Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease

James E. Dahlman et al.

NATURE BIOTECHNOLOGY (2015)

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Article Multidisciplinary Sciences

Gene pyramiding enhances durable blast disease resistance in rice

Shuichi Fukuoka et al.

SCIENTIFIC REPORTS (2015)

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Review Medicine, Research & Experimental

Off-target Effects in CRISPR/Cas9-mediated Genome Engineering

Xiao-Hui Zhang et al.

MOLECULAR THERAPY-NUCLEIC ACIDS (2015)

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Article Agronomy

Pyramiding of three bacterial blight resistance genes for broad-spectrum resistance in deepwater rice variety, Jalmagna

Sharat Kumar Pradhan et al.

RICE (2015)

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Article Biochemistry & Molecular Biology

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

Seung Woo Cho et al.

GENOME RESEARCH (2014)

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Article Multidisciplinary Sciences

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

Samuel H. Sternberg et al.

NATURE (2014)

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Article Biochemistry & Molecular Biology

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

Baohui Chen et al.

CELL (2013)

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Review Agriculture, Multidisciplinary

Traditional and Modern Plant Breeding Methods with Examples in Rice (Oryza sativa L.)

Flavio Breseghello et al.

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2013)

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Article Biochemistry & Molecular Biology

Mechanism of mismatch recognition revealed by human MutS beta bound to unpaired DNA loops

Shikha Gupta et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2012)

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Article Multidisciplinary Sciences

In planta gene targeting

Friedrich Fauser et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

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Article Multidisciplinary Sciences

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

Martin Jinek et al.

SCIENCE (2012)

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Article Biochemical Research Methods

A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes

Yang Zhang et al.

PLANT METHODS (2011)

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Article Plant Sciences

Generation of Backbone-Free, Low Transgene Copy Plants by Launching T- DNA from the Agrobacterium Chromosome

Heiko Oltmanns et al.

PLANT PHYSIOLOGY (2010)

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Review Biochemistry & Molecular Biology

RNA recognition by 3 '-to-5 ' exonucleases: The substrate perspective

Hend Ibrahim et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2008)

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Review Cell Biology

The highways and byways of mRNA decay

Nicole L. Garneau et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2007)

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Review Biochemical Research Methods

Agrobacterium-mediated genetic transformation of plants:: biology and biotechnology

T Tzfira et al.

CURRENT OPINION IN BIOTECHNOLOGY (2006)

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Article Genetics & Heredity

Toward a theory of marker-assisted gene pyramiding

B Servin et al.

GENETICS (2004)

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Article Biochemistry & Molecular Biology

Transgene integration, organization and interaction in plants

A Kohli et al.

PLANT MOLECULAR BIOLOGY (2003)

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Review Microbiology

Agobacterium-mediated plant transformation:: The biology behind the gene-Jockeying tool

SB Gelvin

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2003)

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Article Biochemistry & Molecular Biology

Okazaki fragment maturation in yeast - I. Distribution of functions between FEN1 AND DNA2

R Ayyagari et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

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Article Biochemistry & Molecular Biology

Cre recombinase-mediated inversion using lox66 and lox71: method to introduce conditional point mutations into the CREB-binding protein

ZW Zhang et al.

NUCLEIC ACIDS RESEARCH (2002)

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Article Biochemistry & Molecular Biology

The role of template-primer in protection of reverse transcriptase from thermal inactivation

GF Gerard et al.

NUCLEIC ACIDS RESEARCH (2002)

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Article Multidisciplinary Sciences

RPA governs endonuclease switching during processing of Okazaki fragments in eukaryotes

SH Bae et al.

NATURE (2001)

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