4.7 Article

Prime Editing in the model plant Physcomitrium patens and its potential in the tetraploid potato

Related references

Note: Only part of the references are listed.
Letter Biotechnology & Applied Microbiology

Precise genome modification in tomato using an improved prime editing system

Yuming Lu et al.

PLANT BIOTECHNOLOGY JOURNAL (2021)

Article Engineering, Biomedical

A web tool for the design of prime-editing guide RNAs

Ryan D. Chow et al.

Summary: Prime editing allows diverse genomic alterations to be made at target sites without double-strand breaks or donor templates. However, designing pegRNAs can be complex and time-consuming, as they require customization for each edit. The web tool pegFinder facilitates the rapid design of pegRNAs for downstream experimentation, with the incorporation of sgRNA predictions and nomination of secondary nicking sgRNAs for improved editing efficiency.

NATURE BIOMEDICAL ENGINEERING (2021)

Article Plant Sciences

A blueprint for gene function analysis through Base Editing in the model plant Physcomitrium (Physcomitrella) patens

Anouchka Guyon-Debast et al.

Summary: CRISPR-Cas9 base editors can achieve efficient and precise single-base mutations in Physcomitrium patens, facilitating gene functional analysis and enabling the production of randomly mutagenized variants of a specific gene through multiple sgRNA base editing. The development of a co-editing selection system further enhances the efficiency of site-specific base editing in P. patens.

NEW PHYTOLOGIST (2021)

Article Multidisciplinary Sciences

Precise genome engineering in Drosophila using prime editing

Justin A. Bosch et al.

Summary: The study successfully applied prime editing in Drosophila to introduce premature stop codons and achieve efficient germline transmission, demonstrating its potential for studying gene function in Drosophila.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemical Research Methods

Novel CRISPR/Cas applications in plants: from prime editing to chromosome engineering

Teng-Kuei Huang et al.

Summary: In recent years, significant progress has been made in the field of plant genome editing using CRISPR/Cas technology. This includes the application of both natural and engineered Cas proteins, as well as the development of various gene editing techniques in plants.

TRANSGENIC RESEARCH (2021)

Article Multidisciplinary Sciences

PrimeDesign software for rapid and simplified design of prime editing guide RNAs

Jonathan Y. Hsu et al.

Summary: Prime editing guide RNA design is more complex than for standard CRISPR-based nucleases or base editors. Here the authors present PrimeDesign and PrimeVar for the rapid and simplified design of pegRNA and ngRNA combinations. PrimeVar is a comprehensive and searchable database that includes candidate pegRNA and ngRNA combinations for installing or correcting >68,500 pathogenic human genetic variants.

NATURE COMMUNICATIONS (2021)

Article Biotechnology & Applied Microbiology

High-efficiency prime editing with optimized, paired pegRNAs in plants

Qiupeng Lin et al.

Summary: Designing prime binding sites with a certain melting temperature and using two pegRNAs can substantially enhance the efficiency of prime editing.

NATURE BIOTECHNOLOGY (2021)

Article Biotechnology & Applied Microbiology

Genome-wide specificity of prime editors in plants

Shuai Jin et al.

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.

NATURE BIOTECHNOLOGY (2021)

Letter Biotechnology & Applied Microbiology

Highly efficient C-to-T and A-to-G base editing in a Populus hybrid

Gen Li et al.

PLANT BIOTECHNOLOGY JOURNAL (2021)

Article Biochemistry & Molecular Biology

Prime editing - an update on the field

Janine Scholefield et al.

GENE THERAPY (2021)

Article Biochemistry & Molecular Biology

pegIT - a web-based design tool for prime editing

Mads Valdemar Anderson et al.

Summary: Prime editing is a precise genome editing technology that uses pegRNAs as guide molecules and editing templates. pegIT is a user-friendly web tool for rapid design of various user-defined edits.

NUCLEIC ACIDS RESEARCH (2021)

Article Plant Sciences

Genome- and transcriptome-wide off-target analyses of an improved cytosine base editor

Linnell Bentley Randall et al.

Summary: The study utilized the A3A/Y130F-BE3 system for efficient C-to-T base editing in tomato and analyzed the edited plants at the genome and transcriptome levels, finding no clear off-target effects. Base-edited plants showed higher levels of SNVs and indels compared to control plants, but there was no significant evidence of distinct off-target effects.

PLANT PHYSIOLOGY (2021)

Review Plant Sciences

Precise plant genome editing using base editors and prime editors

Kutubuddin A. Molla et al.

Summary: The development of CRISPR-Cas systems has revolutionized genome editing in plant genetics and breeding. The inefficiency of HDR in many plant species has led to the development of base editing and prime editing technologies, which allow for precise changes at a single-base resolution in the target genome. This Review provides an overview of the current status of base editors and prime editors in plants, covering both technological developments and biological applications.

NATURE PLANTS (2021)

Article Biochemistry & Molecular Biology

PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing

Gue-Ho Hwang et al.

Summary: Prime editing technology allows targeted insertions, deletions, and base conversions, but designing pegRNAs and evaluating high-throughput sequencing data can be complex. Researchers have developed two user-friendly web-based tools, PE-Designer for pegRNA selection and PE-Analyzer for outcome analysis.

NUCLEIC ACIDS RESEARCH (2021)

Article Biotechnology & Applied Microbiology

Prime editing in mice reveals the essentiality of a single base in driving tissue-specific gene expression

Pan Gao et al.

Summary: In mice, both the PE2 and HDR systems led to cell-specific loss of expression of an mRNA/long noncoding RNA gene pair with single nucleotide variants in TFBS. However, PE2 showed higher editing efficiency and lower off-target mutation risk compared to HDR.

GENOME BIOLOGY (2021)

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)

Article Biochemistry & Molecular Biology

Expanding the CRISPR Toolbox in P. patens Using SpCas9-NG Variant and Application for Gene and Base Editing in Solanaceae Crops

Florian Veillet et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Letter Biotechnology & Applied Microbiology

Precision genome engineering in rice using prime editing system

Kai Hua et al.

PLANT BIOTECHNOLOGY JOURNAL (2020)

Letter Biochemistry & Molecular Biology

Plant Prime Editors Enable Precise Gene Editing in Rice Cells

Xu Tang et al.

MOLECULAR PLANT (2020)

Letter Biochemistry & Molecular Biology

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

Huiyuan Li et al.

MOLECULAR PLANT (2020)

Letter Biochemistry & Molecular Biology

Versatile Nucleotides Substitution in Plant Using an Improved Prime Editing System

Wen Xu et al.

MOLECULAR PLANT (2020)

Article Biotechnology & Applied Microbiology

Prime genome editing in rice and wheat

Qiupeng Lin et al.

NATURE BIOTECHNOLOGY (2020)

Review Biochemistry & Molecular Biology

Precision Breeding Made Real with CRISPR: Illustration through Genetic Resistance to Pathogens

Florian Veillet et al.

PLANT COMMUNICATIONS (2020)

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)

Article Biochemistry & Molecular Biology

Development of Plant Prime-Editing Systems for Precise Genome Editing

Rongfang Xu et al.

PLANT COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

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

Andrew V. Anzalone et al.

NATURE (2019)

Article Biochemistry & Molecular Biology

Transgene-Free Genome Editing in Tomato and Potato Plants Using Agrobacterium-Mediated Delivery of a CRISPR/Cas9 Cytidine Base Editor

Florian Veillet et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Biochemistry & Molecular Biology

CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens

Jean-Paul Concordet et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Multidisciplinary Sciences

The CRISPR tool kit for genome editing and beyond

Mazhar Adli

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

Alexis C. Komor et al.

NATURE (2016)

Review Biotechnology & Applied Microbiology

The CRISPR/Cas9 system for plant genome editing and beyond

Luisa Bortesi et al.

BIOTECHNOLOGY ADVANCES (2015)

Review Microbiology

An updated evolutionary classification of CRISPR-Cas systems

Kira S. Makarova et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Biotechnology & Applied Microbiology

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

Yanfang Fu et al.

NATURE BIOTECHNOLOGY (2013)

Article Biochemistry & Molecular Biology

Phytozome: a comparative platform for green plant genomics

David M. Goodstein et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

A novel mutated acetolactate synthase gene conferring specific resistance to pyrimidinyl carboxy herbicides in rice

Ayako Okuzaki et al.

PLANT MOLECULAR BIOLOGY (2007)

Review Plant Sciences

Single-nucleotide mutations for plant functional genomics

S Henikoff et al.

ANNUAL REVIEW OF PLANT BIOLOGY (2003)