Optimized prime editing in monocot plants using PlantPegDesigner and engineered plant prime editors (ePPEs)

Jin, Shuai; Lin, Qiupeng; Gao, Qiang; Gao, Caixia

doi:10.1038/s41596-022-00773-9

Cited by 29 publications

(19 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nevertheless, recent data indicates that the RNase H‐truncated RT variant might be the most suitable option for unstructured RT templates (Doman et al ., 2023 ). In addition, Ni and coworkers recently showed that adding the V223A mutation to the eRT version further enhanced the plant (rice) codon‐optimized PE (PPE) (Lin et al ., 2020 ) and engineered PPE (ePPE) (Jin et al ., 2023 ; Zong et al ., 2022 ) efficiency up to 33‐fold and 6.4‐fold, respectively, in wheat (Ni et al ., 2023 ).…”

Section: Insight Into the Pe Mechanismmentioning

confidence: 99%

Prime editing: Mechanism insight and recent applications in plants

Vu,

Nguyen,

Kim

et al. 2023

Plant Biotechnology Journal

View full text Add to dashboard Cite

SummaryPrime editing (PE) technology utilizes an extended prime editing guide RNA (pegRNA) to direct a fusion peptide consisting of nCas9 (H840) and reverse transcriptase (RT) to a specific location in the genome. This enables the installation of base changes at the targeted site using the extended portion of the pegRNA through RT activity. The resulting product of the RT reaction forms a 3′ flap, which can be incorporated into the genomic site through a series of biochemical steps involving DNA repair and synthesis pathways. PE has demonstrated its effectiveness in achieving almost all forms of precise gene editing, such as base conversions (all types), DNA sequence insertions and deletions, chromosomal translocation and inversion and long DNA sequence insertion at safe harbour sites within the genome. In plant science, PE could serve as a groundbreaking tool for precise gene editing, allowing the creation of desired alleles to improve crop varieties. Nevertheless, its application has encountered limitations due to efficiency constraints, particularly in dicotyledonous plants. In this review, we discuss the step‐by‐step mechanism of PE, shedding light on the critical aspects of each step while suggesting possible solutions to enhance its efficiency. Additionally, we present an overview of recent advancements and future perspectives in PE research specifically focused on plants, examining the key technical considerations of its applications.

show abstract

Section: Insight Into the Pe Mechanismmentioning

confidence: 99%

Prime editing: Mechanism insight and recent applications in plants

Vu,

Nguyen,

Kim

et al. 2023

Plant Biotechnology Journal

View full text Add to dashboard Cite

show abstract

“…The long-sought goal of biologists and crop breeders is to be able to precisely target and modify genes or genomes in living organisms. PE technology represents a significant advance toward achieving this capability ( Jin et al., 2023 ). Over the past 3 years, remarkable progress has been made in enhancing PE efficiency in plants, elevating it from below 5% to nearly 100% ( Jiang et al., 2020 ; Lin et al., 2020 , 2021 ; Xu et al., 2020 , 2021 ; Molla et al., 2021 ; Wang et al., 2021 ; Li et al., 2022a , 2022b ; Zong et al., 2022 ; Gupta et al., 2023b ; Jin et al., 2023 ; Ni et al., 2023 ; Qiao et al., 2023 ).…”

Section: Discussionmentioning

confidence: 99%

“…PE technology represents a significant advance toward achieving this capability ( Jin et al., 2023 ). Over the past 3 years, remarkable progress has been made in enhancing PE efficiency in plants, elevating it from below 5% to nearly 100% ( Jiang et al., 2020 ; Lin et al., 2020 , 2021 ; Xu et al., 2020 , 2021 ; Molla et al., 2021 ; Wang et al., 2021 ; Li et al., 2022a , 2022b ; Zong et al., 2022 ; Gupta et al., 2023b ; Jin et al., 2023 ; Ni et al., 2023 ; Qiao et al., 2023 ). This advance has now paved the way for efficient multigene targeting, a breakthrough that we demonstrate in this study.…”

Section: Discussionmentioning

confidence: 99%

Modularly assembled multiplex prime editors for simultaneous editing of agronomically important genes in rice

Gupta,

Liu,

Raza

et al. 2024

Plant Communications

View full text Add to dashboard Cite

“…Therefore, we need to go from cis and use gene editing to knock out these SEs or mutants with T-DNA insertions to disrupt SE structures to examine their expression change patterns for nearby potential target genes. Specifically, more nuanced manipulation of such SEs may be possible in the future using gene insertion and deletion tools that involve prime editing 57 , along with programmable addition via site-specific targeting elements (PASTE) 58 .…”

Section: Discussionmentioning

confidence: 99%

Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL

Sun,

Zhou,

et al. 2024

Nat Commun

View full text Add to dashboard Cite

Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.

show abstract

Optimized prime editing in monocot plants using PlantPegDesigner and engineered plant prime editors (ePPEs)

Cited by 29 publications

References 60 publications

Prime editing: Mechanism insight and recent applications in plants

Prime editing: Mechanism insight and recent applications in plants

Modularly assembled multiplex prime editors for simultaneous editing of agronomically important genes in rice

Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL

Contact Info

Product

Resources

About