CRISPR Journal最新文献

Strategies and Protocols for Optimized Genome Editing in Potato. 马铃薯基因组编辑优化策略与方案

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-02-01 Epub Date: 2024-12-04 DOI: 10.1089/crispr.2024.0068

Frida Meijer Carlsen, Ida Westberg, Ida Elisabeth Johansen, Erik Andreasson, Bent Larsen Petersen

{"title":"Strategies and Protocols for Optimized Genome Editing in Potato.","authors":"Frida Meijer Carlsen, Ida Westberg, Ida Elisabeth Johansen, Erik Andreasson, Bent Larsen Petersen","doi":"10.1089/crispr.2024.0068","DOIUrl":"10.1089/crispr.2024.0068","url":null,"abstract":"The potato family includes a highly diverse cultivar repertoire and has a high potential for nutritional yield improvement and refinement but must in line with other crops be adapted to biotic and abiotic stresses, for example, accelerated by climate change and environmental demands. The combination of pluripotency, high ploidy, and relative ease of protoplast isolation, transformation, and regeneration together with clonal propagation through tubers makes potato highly suitable for precise genetic engineering. Most potato varieties are tetraploid having a very high prevalence of length polymorphisms and small nucleotide polymorphisms between alleles, often complicating CRISPR-Cas editing designs and strategies. CRISPR-Cas editing in potato can be divided into (i) characterization of target area and in silico-aided editing design, (ii) isolation and editing of protoplast cells, and (iii) the subsequent explant regeneration from single protoplast cells. Implementation of efficient CRISPR-Cas editing relies on efficient editing at the protoplast (cell pool) level and on robust high-throughput editing scoring methods at the cell pool and explant level. Gene and chromatin structure are additional features to optionally consider. Strategies and solutions for addressing key steps in genome editing of potato, including light conditions and schemes for reduced exposure to hormones during explant regeneration, which is often linked to somaclonal variation, are highlighted.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"37-50"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Acknowledgment of Reviewers 2024.

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-02-01 DOI: 10.1089/crispr.2024.03520.revack

引用次数: 0

Managing Expectations for CRISPR in a Volatile World.

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-02-01 Epub Date: 2025-01-23 DOI: 10.1089/crispr.2025.0006

Rodolphe Barrangou

引用次数: 0

Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA.

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-02-01 Epub Date: 2025-01-06 DOI: 10.1089/crispr.2024.0050

Anya Kardailsky, Benjamín Durán-Vinet, Georgia Nester, Marcelle E Ayad, Eric J Raes, Gert-Jan Jeunen, Allison K Miller, Philip McVey, Shannon Corrigan, Matthew Fraser, Priscila Goncalves, Stephen Burnell, Adam Bennett, Sebastian Rauschert, Philipp E Bayer

{"title":"Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA.","authors":"Anya Kardailsky, Benjamín Durán-Vinet, Georgia Nester, Marcelle E Ayad, Eric J Raes, Gert-Jan Jeunen, Allison K Miller, Philip McVey, Shannon Corrigan, Matthew Fraser, Priscila Goncalves, Stephen Burnell, Adam Bennett, Sebastian Rauschert, Philipp E Bayer","doi":"10.1089/crispr.2024.0050","DOIUrl":"https://doi.org/10.1089/crispr.2024.0050","url":null,"abstract":"Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA biomonitoring is limited by biases toward certain species and the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics of eDNA enables the collection of whole ecosystem data by sequencing all molecules present, allowing characterization and identification. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas)-based methods have the potential to improve the efficiency of eDNA metagenomic sequencing of low-abundant target organisms and simplify data analysis by enrichment of target species or nontarget DNA depletion before sequencing. Implementation of CRISPR-Cas in eDNA has been limited due to a lack of interest and support in the past. This perspective synthesizes current approaches of CRISPR-Cas to study underrepresented taxa and advocate for further application and optimization of depletion and enrichment methods of eDNA using CRISPR-Cas, holding promise for eDNA biomonitoring.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"8 1","pages":"5-12"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CRISPR-Cas9-Mediated Correction of TSC2 Pathogenic Variants in iPSCs from Patients with Tuberous Sclerosis Complex Type 2. crispr - cas9介导的2型结节性硬化症患者iPSCs中TSC2致病变异的校正

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-02-01 Epub Date: 2024-12-10 DOI: 10.1089/crispr.2024.0079

Gongbo Guo, Morgan Moser, Lincoln Chifamba, Dominic Julian, Samantha Teierle, Prajwal Rajappa, Cecelia Miller, Mark E Hester

{"title":"CRISPR-Cas9-Mediated Correction of TSC2 Pathogenic Variants in iPSCs from Patients with Tuberous Sclerosis Complex Type 2.","authors":"Gongbo Guo, Morgan Moser, Lincoln Chifamba, Dominic Julian, Samantha Teierle, Prajwal Rajappa, Cecelia Miller, Mark E Hester","doi":"10.1089/crispr.2024.0079","DOIUrl":"10.1089/crispr.2024.0079","url":null,"abstract":"Tuberous sclerosis complex (TSC) is an autosomal dominant disorder caused by mutations in either the TSC1 or TSC2 genes. Though TSC causes the formation of nonmalignant tumors throughout multiple organs, the most frequent causes of mortality and morbidity are due to neurological complications. In two-thirds of cases, TSC occurs sporadically and TSC2 pathogenic variants are approximately three times more prevalent than TSC1 pathogenic variants. Here, we utilized CRISPR-Cas9-mediated homology directed repair in patient induced pluripotent stem cells (iPSCs) to correct two types of TSC2 pathogenic variants generating two isogenic lines. In one line, we corrected a splice acceptor variant (c.2743-1G>A), which causes the skipping of coding exon 23 and subsequent frameshift and introduction of a stop codon in coding exon 25. In the second line, we corrected a missense variant in coding exon 40 within the GTPase-activating protein domain (c.5228G>A, p.R1743Q). The generation of TSC2 patient iPSCs in parallel with their corresponding CRISPR-corrected isogenic lines will be an important tool for disease modeling applications and for developing therapeutics.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"60-70"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142802489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Establishment of a CRISPR-Cas9-Mediated Genome Editing System in Flax. crispr - cas9介导的亚麻基因组编辑系统的建立

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-02-01 Epub Date: 2025-01-13 DOI: 10.1089/crispr.2024.0064

Chunming Wang, Chao Sun, Li Shi, Jiannan Zhou, Shuai Liu, Yongsheng Bai, Weichang Yu

{"title":"Establishment of a CRISPR-Cas9-Mediated Genome Editing System in Flax.","authors":"Chunming Wang, Chao Sun, Li Shi, Jiannan Zhou, Shuai Liu, Yongsheng Bai, Weichang Yu","doi":"10.1089/crispr.2024.0064","DOIUrl":"10.1089/crispr.2024.0064","url":null,"abstract":"Flax is an important crop used for oil and fiber production. Although genetic engineering has been possible in flax, it is not commonly used to produce cultivars. However, the use of genome editing technology, which can produce site-specific mutations without introducing foreign genes, may be a valuable tool for creating elite cultivars that can be easily cultivated. The purpose of this study was to investigate the potential of genome editing in flax by establishing the clustered regularly interspaced short palindromic repeats (CR ISPR)-CRISPR-associated protein 9 (CRISPR-Cas9) genome editing system using the phytoene desaturase (PDS) gene, which produces albino mutants that are easily identifiable. Four sgRNAs were designed from two PDS genes of Flax (LuPDS1 and LuPDS2), and CRISPR-Cas9 genome editing vectors were constructed. After gene transformation, albino phenotypes were observed in transformed callus and regenerated plantlets on selection media. Polymerase chain reaction (PCR) amplification and sequencing of the PDS genes revealed deletions and insertions in the albino tissues, indicating successful editing of the PDS genes. Potential off-target sites were analyzed, but no off-target mutations were found, indicating the specificity of the CRISPR-Cas9 system. The establishment of a flax genome editing system using the CRISPR-Cas9 technology opens up new possibilities for the genetic engineering of flax. This study demonstrates the potential of genome editing in creating elite cultivars that can be easily cultivated, which can have significant implications for the flax industry.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"51-59"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Efficient Generation of SOCS2 Knock-Out Sheep by Electroporation of CRISPR-Cas9 Ribonucleoprotein Complex with Dual-sgRNAs. 用双sgrnas电穿孔CRISPR-Cas9核糖核蛋白复合物高效产生SOCS2基因敲除羊。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-02-01 Epub Date: 2025-01-14 DOI: 10.1089/crispr.2024.0055

Ahmed K Mahdi, Devon S Fitzpatrick, Darren E Hagen, Bret R McNabb, Tara Urbano Beach, William M Muir, Nicholas Werry, Alison L Van Eenennaam, Juan F Medrano, Pablo J Ross

{"title":"Efficient Generation of SOCS2 Knock-Out Sheep by Electroporation of CRISPR-Cas9 Ribonucleoprotein Complex with Dual-sgRNAs.","authors":"Ahmed K Mahdi, Devon S Fitzpatrick, Darren E Hagen, Bret R McNabb, Tara Urbano Beach, William M Muir, Nicholas Werry, Alison L Van Eenennaam, Juan F Medrano, Pablo J Ross","doi":"10.1089/crispr.2024.0055","DOIUrl":"10.1089/crispr.2024.0055","url":null,"abstract":"In mice, naturally occurring and induced mutations in the suppressor of cytokine signaling-2 (Socs2) gene are associated with a high growth phenotype characterized by rapid post-weaning weight gain and 30-50% heavier mature body weight. In this work, we demonstrate an electroporation-based method of producing SOCS2 knock-out (KO) sheep. Electroporation of dual-guide CRISPR-Cas9 ribonucleoprotein complexes targeting SOCS2 was performed 6 h post-fertilization in sheep zygotes. Fifty-two blastocysts were transferred to 13 estrus-synchronized recipients, yielding five live lambs and one stillborn. These lambs all carried mutations predicted to result in SOCS2 KO. Three carried large deletion alleles which evaded detection in initial PCR screening. Off-target analysis using whole genome sequencing comparing the frequency of mutations in regions within 100 bp of possible sgRNA binding sites (up to 4 bp mismatches) and elsewhere in the genome showed no significant difference when comparing unedited control sheep to edited animals (p = 0.71). In conclusion, electroporation of zygotes with dual-guide CRISPR-Cas9 RNPs was effective at generating knock-out sheep with no substantial off-target activity.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"13-25"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142980871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

From Code to Comprehension: AI Captures the Language of Life.

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-02-01 Epub Date: 2025-01-29 DOI: 10.1089/crispr.2025.0008

Luis E Valentin-Alvarado, Gavin J Knott

引用次数: 0

An Efficient and Cost-Effective Novel Strategy for Identifying CRISPR-Cas-Mediated Mutants in Plant Offspring. 在植物后代中鉴定crispr - cas介导的突变体的一种高效且经济的新策略。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-02-01 Epub Date: 2025-01-13 DOI: 10.1089/crispr.2024.0057

Xueting Liu, Li Huang, Meng Li, Ying Fu, Wei Zhang, Sen Zhang, Xinyue Liang, Qian Shen

{"title":"An Efficient and Cost-Effective Novel Strategy for Identifying CRISPR-Cas-Mediated Mutants in Plant Offspring.","authors":"Xueting Liu, Li Huang, Meng Li, Ying Fu, Wei Zhang, Sen Zhang, Xinyue Liang, Qian Shen","doi":"10.1089/crispr.2024.0057","DOIUrl":"10.1089/crispr.2024.0057","url":null,"abstract":"The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system has revolutionized targeted mutagenesis, but screening for mutations in large sample pools can be time-consuming and costly. We present an efficient and cost-effective polymerase chain reaction (PCR)-based strategy for identifying edited mutants in the T1 generation. Unlike previous methods, our approach addresses the challenges of large progeny populations by using T0 generation sequencing results for genotype prediction. The T1 generation plants were then divided into two scenarios: ≥4 bp indels and 1-2 bp indels. Specific primers are designed for these categories, employing dual-primers critical annealing temperature PCR for ≥4 bp indels and the derived cleaved amplified polymorphic sequences (dCAPS) method for 1-2 bp indels. This method is straightforward, cost-effective, and allows rapid and precise identification of T1 editing outcomes, distinguishing between wild-type, heterozygous, and homozygous plants. This strategy accelerates gene functional analysis in plants and beyond.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"26-36"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Response to Cook et al. re: Novel Off-Targeting Events Identified After Genome Wide Analysis of CRISPR-Cas Edited Pig. 对 Cook 等人的回应：对 CRISPR-Cas 编辑过的猪进行全基因组分析后发现的新脱靶事件。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-01-27 DOI: 10.1089/crispr.2025.0003

Bethany K Redel, Kiho Lee

引用次数: 0