SpRY greatly expands the genome editing scope in rice with highly flexible PAM recognition

Xu, Ziyan; Kuang, Yongjie; Ren, Bin; Yan, Daqi; Yan, Fang; Spetz, Carl; Sun, Wenxian; Wang, Guirong; Zhou, Xueping; Zhou, Huanbin

doi:10.1101/2020.09.23.310839

Cited by 4 publications

(4 citation statements)

References 41 publications

(61 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“… 31 In the future, it will be worthwhile to attempt this experiment again with base editors, such as evoAPOBEC1-BE4max and BE4-SsAPOBEC3B models, which have been designed with these new enzymes (allowing high and precise deamination and reducing off targets), or NG-Cas9, SpG, and SpRY (having a non-specific PAM). 22 , 33 , 34 , 35 These enzymes have also been designed to have a narrower conversion window, which could be used to favor C2 editing. We hope that the recent development of the Prime editing technology might allow us to modify only the C2 nucleotide.…”

Section: Discussionmentioning

confidence: 99%

Base editing strategy for insertion of the A673T mutation in the APP gene to prevent the development of AD in vitro

Guyon

Rousseau

Bégin

et al. 2021

Molecular Therapy - Nucleic Acids

View full text Add to dashboard Cite

The amyloid precursor protein ( APP ) is a transmembrane protein mostly found in neurons. Cleavage of this protein by β-secretase can lead to the formation of amyloid-β (Aβ) peptide plaque, which leads to Alzheimer’s disease. Genomic analysis of an Icelandic population that did not show symptoms of Alzheimer’s at an advanced age led to the discovery of the A673T mutation. This mutation can reduce β-secretase cleavage by 40%. We hypothesized that the insertion of this mutation in patients’ neurons could be an effective and sustainable method of slowing down or even stopping the progression of Alzheimer’s disease. We modified the APP gene in HEK293T cells and in SH-SY5Y neuroblastoma using a Cas9 nickase (Cas9n)-deaminase enzyme to convert the alanine codon to a threonine. Several Cas9n-deaminase variants were tested to compare their efficiency of conversion. The results were characterized and quantified by deep sequencing. We successfully introduced the A673T mutation in 53% of HEK293T cells alongside a new mutation (E674K), which seemed to further reduce Aβ peptide accumulation. Our approach aimed to provide a new strategy for the treatment of Alzheimer’s and in so doing, demonstrate the capacity of base editing techniques for treating genetic diseases.

show abstract

Section: Discussionmentioning

confidence: 99%

Base editing strategy for insertion of the A673T mutation in the APP gene to prevent the development of AD in vitro

Guyon

Rousseau

Bégin

et al. 2021

Molecular Therapy - Nucleic Acids

View full text Add to dashboard Cite

show abstract

“…For example, Cas9-NG, ScCas9 and iSpyMacCas9 were applied to plants, using NG, NAG, and NAAR PAMs, respectively (Hua et al 2019;Sretenovic et al 2020;Wang et al 2020c). Also, the development of SpRY with very low PAM restriction was applicable for BEs in plants (Ren et al 2021;Walton et al 2020;Xu et al 2021). BE by Cas12a or its PAM altered variants has been successfully performed in human cells (Kleinstiver et al 2019;Li et al 2018a), but has not been reported in plants to date.…”

Section: Advances Of the Base Editing Techniquementioning

confidence: 99%

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

Huang

Puchta

2021

Transgenic Res

View full text Add to dashboard Cite

In the last years, tremendous progress has been made in the development of CRISPR/Cas-mediated genome editing tools. A number of natural CRISPR/Cas nuclease variants have been characterized. Engineered Cas proteins have been developed to minimize PAM restrictions, off-side effects and temperature sensitivity. Both kinds of enzymes have, by now, been applied widely and efficiently in many plant species to generate either single or multiple mutations at the desired loci by multiplexing. In addition to DSB-induced mutagenesis, specifically designed CRISPR/Cas systems allow more precise gene editing, resulting not only in random mutations but also in predefined changes. Applications in plants include gene targeting by homologous recombination, base editing and, more recently, prime editing. We will evaluate these different technologies for their prospects and practical applicability in plants. In addition, we will discuss a novel application of the Cas9 nuclease in plants, enabling the induction of heritable chromosomal rearrangements, such as inversions and translocations. This technique will make it possible to change genetic linkages in a programmed way and add another level of genome engineering to the toolbox of plant breeding. Also, strategies for tissue culture free genome editing were developed, which might be helpful to overcome the transformation bottlenecks in many crops. All in all, the recent advances of CRISPR/Cas technology will help agriculture to address the challenges of the twenty-first century related to global warming, pollution and the resulting food shortage.

show abstract

“…The researchers further optimized SpG to develop SpRY that has the potential of targeting almost all PAM. Xu et al (2020a) have researched the effectiveness of both SpG and SpRY nucleases against separate PAMs and their use in both cytosine and adenine base editing using transgenic rice callus. They reported that even though SpG recognizes NG PAM sequences, its performance is less when compared to SpCas9-NG in rice.…”

Section: Pamless Base Editorsmentioning

confidence: 99%

Base Editing in Plants: Applications, Challenges, and Future Prospects

Azameti

Palnam

2021

Front. Plant Sci.

View full text Add to dashboard Cite

The ability to create targeted modifications in the genomes of plants using genome editing technologies has revolutionized research in crop improvement in the current dispensation of molecular biology. This technology has attracted global attention and has been employed in functional analysis studies in crop plants. Since many important agronomic traits are confirmed to be determined by single-nucleotide polymorphisms, improved crop varieties could be developed by the programmed and precise conversion of targeted single bases in the genomes of plants. One novel genome editing approach which serves for this purpose is base editing. Base editing directly makes targeted and irreversible base conversion without creating double-strand breaks (DSBs). This technology has recently gained quick acceptance and adaptation because of its precision, simplicity, and multiplex capabilities. This review focuses on generating different base-editing technologies and how efficient they are in editing nucleic acids. Emphasis is placed on the exploration and applications of these base-editing technologies to enhance crop production. The review also highlights the drawbacks and the prospects of this new technology.

show abstract

SpRY greatly expands the genome editing scope in rice with highly flexible PAM recognition

Cited by 4 publications

References 41 publications

Base editing strategy for insertion of the A673T mutation in the APP gene to prevent the development of AD in vitro

Base editing strategy for insertion of the A673T mutation in the APP gene to prevent the development of AD in vitro

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

Base Editing in Plants: Applications, Challenges, and Future Prospects

Contact Info

Product

Resources

About