Mario Gründlinger, Chiara Ellensohn, Leo Drechsel, Ulrike Schreiner, Siebe Pierson, Clara Baldin, Susanne Zeilinger
{"title":"Simply cut out - Combining CRISPR/Cas9 RNPs and transiently selected telomere vectors for marker free-gene deletion in <i>Trichoderma atroviride</i>.","authors":"Mario Gründlinger, Chiara Ellensohn, Leo Drechsel, Ulrike Schreiner, Siebe Pierson, Clara Baldin, Susanne Zeilinger","doi":"10.3389/fgeed.2025.1623963","DOIUrl":"10.3389/fgeed.2025.1623963","url":null,"abstract":"<p><p><i>Trichoderma atroviride</i> is a well-known mycoparasitic fungus widely used for the biological control of fungal plant pathogens. However, genetic manipulation in this organism remains challenging due to the limited availability of versatile and efficient molecular tools. Here, we present a CRISPR/Cas9-based method for targeted gene manipulation using ribonucleoprotein (RNP) complexes combined with a transiently stable telomere vector. We successfully inactivated three genes-<i>pks4</i> (spore pigment production), <i>pyr4</i> (pyrimidine biosynthesis), and <i>pex5</i> (peroxisomal matrix protein import receptor)-to demonstrate the system's utility. Although double-strand breaks induced by Cas9 can be repaired via homology-directed repair (HDR), using donor templates, the most effective gene inactivations in our case were achieved via non-homologous end joining (NHEJ), by co-transforming the transiently stable telomere vector carrying the hygromycin-resistance gene (<i>hph</i>), which was rapidly lost under non-selective conditions. This strategy enables marker-free genetic manipulation, supports vector recycling, and simplifies successive transformations. Overall, our method expands the genetic toolbox for <i>T. atroviride</i>, offering a fast and reliable approach for reverse genetics in this agriculturally important fungus.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1623963"},"PeriodicalIF":4.9,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12263576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144651405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tushadri Singh, H M Mamrutha, Rajender Singh, J P Jaiswal, Zeenat Wadhwa, Rakesh Kumar, Omvir Singh, O P Ahlawat, Ratan Tiwari
{"title":"Comprehensive approaches to design efficient gRNA for SDN1-CRISPR/Cas9 genome editing in wheat.","authors":"Tushadri Singh, H M Mamrutha, Rajender Singh, J P Jaiswal, Zeenat Wadhwa, Rakesh Kumar, Omvir Singh, O P Ahlawat, Ratan Tiwari","doi":"10.3389/fgeed.2025.1579165","DOIUrl":"10.3389/fgeed.2025.1579165","url":null,"abstract":"<p><strong>Background: </strong>CRISPR/Cas9 technology has gained popularity due to its efficient, widely applicable, and relatively easy genome editing. Furthermore, the removal of regulation on site-directed nuclease1- (SDN1) and SDN2-developed products in many countries has made it a more revolutionary technology for adoption in crop improvement. Designing accurate guide RNA (gRNA) is the initial and most crucial step that decides the success of the editing. Although the gene editing technique is widely used in crops, a detailed and comprehensive method for designing efficient gRNA in wheat is still lacking. By virtue of wheat being a hexaploid crop and having a large genome size with repetitive DNA, a tailor-made strategy for designing the gRNA is crucial.</p><p><strong>Result: </strong>The manuscript explains the comprehensive strategies and methods for efficient gRNA designing by considering the physical and structural expression of the target gene in the genome and explains the on-target and off-target effects of gRNA for its precise editing through the CRISPR/Cas9-mediated SDN1 method of genome editing in wheat.</p><p><strong>Conclusion: </strong>The present manuscript is first of its kind to address the holistic approach, starting from efficient gene selection, gRNA designing, and post-gRNA designing issues like gRNA stability, binding efficiency, and functionality for SDN1-CRISPR/Cas9 genome editing in wheat. This manuscript will be a ready reference for wheat researchers designing effective gRNA for wheat improvement to meet future food demand.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1579165"},"PeriodicalIF":4.9,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12259558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144644291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"DNA-free CRISPR genome editing in raspberry (<i>Rubus idaeus</i>) protoplast through RNP-mediated transfection.","authors":"Ryan Creeth, Andrew Thompson, Zoltan Kevei","doi":"10.3389/fgeed.2025.1589431","DOIUrl":"10.3389/fgeed.2025.1589431","url":null,"abstract":"<p><p>Protoplast-based systems have been utilised in a wide variety of plant species to enable genome editing without chromosomal introgression of foreign DNA into plant genomes. DNA-free genome editing followed by protoplast regeneration allows elite cultivars to be edited without further genetic segregation, preserving their unique genetic composition and their regulatory status as non-transgenic. However, protoplast isolation presents a barrier to the development of advanced breeding technologies in raspberry and no protocol has been published for DNA-free genome editing in the species. Pre-assembled ribonucleoprotein complexes (RNPs) do not require cellular processing and the commercial availability of Cas9 proteins and synthetic guide RNAs has streamlined genome editing protocols. This study presents a novel high-yielding protoplast isolation protocol from raspberry stem cultures and RNP-mediated transfection of protoplast with CRISPR-Cas9. Targeted mutagenesis of the phytoene desaturase gene at two intragenic loci resulted in an editing efficiency of 19%, though estimated efficiency varied depending on the indel analysis technique. Only amplicon sequencing was sensitive enough to confirm genome editing in a low efficiency sample. To our knowledge, this study constitutes the first use of DNA-free genome editing in raspberry protoplast. This protocol provides a valuable platform for understanding gene function and facilitates the future development of precision breeding in this important soft fruit crop.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1589431"},"PeriodicalIF":4.9,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12256493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144638866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marilu Mestanza, Angel David Hernández-Amasifuen, Alexandra Jherina Pineda-Lázaro, Dennis Eriksson, Juan Carlos Guerrero-Abad
{"title":"Genome editing for sustainable agriculture in Peru: advances, potential applications and regulation.","authors":"Marilu Mestanza, Angel David Hernández-Amasifuen, Alexandra Jherina Pineda-Lázaro, Dennis Eriksson, Juan Carlos Guerrero-Abad","doi":"10.3389/fgeed.2025.1611040","DOIUrl":"10.3389/fgeed.2025.1611040","url":null,"abstract":"<p><p>Peruvian agriculture is characterize by crops such as potato, maize, rice, asparagus, mango, banana, avocado, cassava, onion, oil palm, chili, papikra, blueberry, coffee, cacao, grapes, quinoa, olive, citrus and others. All of them have challenges in production in their specific agroecosystems under stress due to pests, diseases, salinity, drought, cold among others. Gene editing through CRISPR/Cas is a key tool for addressing critical challenges in agriculture by improving resilience to biotic and abiotic stress, increasing yield and enhancing the nutritional value of the crops. This approach allows precise mutation on site-specific gene at the DNA level, obtaining desirable traits when its function is altered. The CRISPR/Cas system could be used as a transgene-free genome editing tool when the ribonucleoprotein (RNP) acts as a carrier to delivered the CRISPR/Cas components into the plant cell protoplasts, or when the tRNA-like sequence (TLS) motifs are fused to single-guide RNA (sgRNA) and Cas mRNA sequence and expressed in transgenic plants rootstock to produce \"mobile\" CRISPR/Cas components to upper tissue (scion). Those innovations could be a potential approach to strengthen the Peruvian agriculture, food security and gricultural economy, especially in the tropical, Andean and coastal regions. This review article examines the advances and strategies of gene editing, focusing on transgene-free methodologies that could be adopted for research, development and use, and also identifies potential applications in key crops for Peru and analyzes their impact in the productivity and reduction of agrochemicals dependence. Finally, this review highlights the need to establish regulatory policies that strengthen the use of biotechnological precise innovations, ensuring the conservation and valorization of agrobiodiversity for the benefit of Peruvian farmers.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1611040"},"PeriodicalIF":4.9,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12258049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144638867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A long shelf-life melon created via CRISPR/Cas9 RNP-based <i>in planta</i> genome editing.","authors":"Kentaro Sasaki, Kaoru Urano, Naozumi Mimida, Satoko Nonaka, Hiroshi Ezura, Ryozo Imai","doi":"10.3389/fgeed.2025.1623097","DOIUrl":"10.3389/fgeed.2025.1623097","url":null,"abstract":"<p><p>Genome editing in melon (<i>Cucumis melo</i> L.) remains a significant challenge due to the inefficiencies associated with conventional cell culture-based transformation methods. In the present study, a novel <i>in planta</i> Particle Bombardment (iPB) approach was developed to enable DNA-free genome editing in melon without the need for cell culture. CRISPR/Cas9 ribonucleoproteins (RNPs) were coated onto gold particles and delivered directly into shoot apical meristem tissue, which harbors potential germline cells, via particle bombardment. This method was applied to enhance fruit shelf-life by targeting an ethylene biosynthesis gene (<i>CmACO1</i>). The resulting <i>cmaco1</i> mutant demonstrated a significantly extended shelf-life, attributable to reduced ethylene production during fruit ripening. This delayed ripening phenotype was reversed upon treatment with exogenous ethylene, confirming the functional impact of <i>CmACO1</i> disruption. Because this strategy bypasses cell culture, the iPB-RNP method offers a solution to common limitations in genome editing, such as genotype dependence and somaclonal variation. Consequently, this technique holds substantial promise for advancing commercial melon breeding efforts and may be broadly applicable to other species within the Cucurbitaceae family.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1623097"},"PeriodicalIF":4.9,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Muhammad W Luqman, Piroon Jenjaroenpun, Jessica Spathos, Nikhil Shingte, Mitchell Cummins, Pattaraporn Nimsamer, Lars M Ittner, Thidathip Wongsurawat, Fabien Delerue
{"title":"Long read sequencing reveals transgene concatemerization and vector sequences integration following AAV-driven electroporation of CRISPR RNP complexes in mouse zygotes.","authors":"Muhammad W Luqman, Piroon Jenjaroenpun, Jessica Spathos, Nikhil Shingte, Mitchell Cummins, Pattaraporn Nimsamer, Lars M Ittner, Thidathip Wongsurawat, Fabien Delerue","doi":"10.3389/fgeed.2025.1582097","DOIUrl":"10.3389/fgeed.2025.1582097","url":null,"abstract":"<p><p>Over the last decade CRISPR gene editing has been successfully used to streamline the generation of animal models for biomedical research purposes. However, one limitation to its use is the potential occurrence of on-target mutations that may be detrimental or otherwise unintended. These bystander mutations are often undetected using conventional genotyping methods. The use of Adeno-Associated Viruses (AAVs) to bring donor templates in zygotes is currently being deployed by transgenic cores around the world to generate knock-ins with large transgenes (i.e., 1-4 kb payloads). Thanks to a high level of efficiency and the relative ease to establish this technique, it recently became a method of choice for transgenic laboratories. However, a thorough analysis of the editing outcomes following this method is yet to be developed. To this end, we generated three different types of integration using AAVs in two different murine genes (i.e., <i>Ace2</i> and <i>Foxg1</i>) and employed Oxford Nanopore Technologies long read sequencing to analyze the outcomes. Using a workflow that includes Cas9 enrichment and adaptive sampling, we showed that unintended on-target mutations, including duplication events and integration of viral sequences (sometimes reported using other workflows) can occur when using AAVs. This work highlights the importance of in-depth validation of the mutant lines generated and informs the uptake of this new method.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1582097"},"PeriodicalIF":4.9,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Srividhya Venkataraman, David Zaruk, Kathleen Hefferon
{"title":"Recent developments, challenges and opportunities in genome editing for crop science from a societal perspective.","authors":"Srividhya Venkataraman, David Zaruk, Kathleen Hefferon","doi":"10.3389/fgeed.2025.1568072","DOIUrl":"10.3389/fgeed.2025.1568072","url":null,"abstract":"<p><p>Genome editing has presented enormous potential in the fields of medicine and agriculture. Here, we explore the social and regulatory aspects of genome editing from the perspective of food security. We provide recent examples of crop genome editing successes. We discuss the current regulatory framework for genome edited crops in North America and Europe, and present how public perception can influence international policies and trade.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1568072"},"PeriodicalIF":4.9,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meredith K Loth, Kendall T Mesch, Celine Herrera-Garcia, Liza E Brusman, Zoe R Donaldson
{"title":"Lentiviral CRISPRa/i in the adult prairie vole brain: modulating neuronal gene expression without DNA cleavage.","authors":"Meredith K Loth, Kendall T Mesch, Celine Herrera-Garcia, Liza E Brusman, Zoe R Donaldson","doi":"10.3389/fgeed.2025.1602983","DOIUrl":"10.3389/fgeed.2025.1602983","url":null,"abstract":"<p><p>Prairie voles (<i>Microtus ochrogaster</i>) are a powerful model for studying the neurobiology of social bonding, yet tools for region- and cell type-specific gene regulation remain underdeveloped in this species. Here, we present a lentivirus-mediated CRISPR activation and interference (CRISPRa/i) platform for somatic gene modulation in the prairie vole brain. This system enables non-mutagenic, titratable regulation of gene expression in the adult brain without germline modification. Our dual-vector system includes one construct expressing dCas9-VPR (VP64-p65-Rta) referred to as CRISPRa or dCas9-KRAB-MeCP2 (Kruppel-associated box-methyl CpG binding protein 2), referred to as CRISPRi under a neuron-specific promoter, and a second construct delivering a U6-driven sgRNA (single guide RNA) alongside an elongation factor 1 alpha (EF1α)-driven mCherry reporter. We detail the design, production, and stereotaxic delivery of these tools and demonstrate their application by targeting four genes implicated in social behavior (<i>Oxtr, Avpr1a, Drd1,</i> and <i>Drd2</i>) across two mesolimbic brain regions: the nucleus accumbens and ventral pallidum. Gene expression analyses confirmed robust, bidirectional transcriptional modulation for selected targets, establishing a proof of concept for CRISPRa/i in this non-traditional model. The dual-vector design is readily adaptable to other gene targets, cell types, and brain regions, and can be multiplexed to provide a flexible and scalable framework for investigating gene function in behaviorally relevant circuits. These advances represent the first successful implementation of somatic CRISPRa/i in prairie voles and expand the genetic toolkit available for this species.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1602983"},"PeriodicalIF":4.9,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12162470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Basavantraya N Devanna, Yugander Arra, Maganti Sheshu Madhav
{"title":"Editorial: Plant breeding innovations-CRISPR as a powerful weapon for agricultural crops.","authors":"Basavantraya N Devanna, Yugander Arra, Maganti Sheshu Madhav","doi":"10.3389/fgeed.2025.1623540","DOIUrl":"10.3389/fgeed.2025.1623540","url":null,"abstract":"","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1623540"},"PeriodicalIF":4.9,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12137227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Base editors in zebrafish: a new era for functional genomics and disease modeling.","authors":"Yuwen Liu, Chao Li, Yiren Qiu, Sihong Chen, Yijun Luo, Donghua Xiong, Jun Zhao, Jianmin Ye, Xuegeng Wang, Wei Qin, Fang Liang","doi":"10.3389/fgeed.2025.1598887","DOIUrl":"10.3389/fgeed.2025.1598887","url":null,"abstract":"<p><p>Base editing has revolutionized genome engineering by enabling precise single-nucleotide modifications without inducing double-strand breaks. As a powerful and efficient gene-editing tool, base editors (BEs) have been widely applied in various model organisms, including zebrafish (<i>Danio rerio</i>), to facilitate functional genomic studies and disease modeling. Zebrafish, with its genetic similarity to humans and rapid development, provides an excellent platform for testing and optimizing emerging base editing technologies. This review comprehensively explores the advancements of cytosine and adenine base editors in zebrafish, highlighting recent developments that enhance efficiency, specificity, and editing scope. We discuss novel base editor variants tailored for zebrafish applications, improvements in delivery strategies, and methodologies to minimize off-target effects. Furthermore, we compare base editing with other precision genome-editing technologies, such as prime editing and homology-directed repair, to underscore its advantages in achieving targeted mutations with high fidelity. By evaluating the expanding role of base editing in zebrafish, this review provides valuable insights into its potential for translational research, genetic disease modeling, and future therapeutic applications.</p>","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"7 ","pages":"1598887"},"PeriodicalIF":4.9,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12133889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}