CRISPR Journal最新文献_第4页

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 : 2025-04-01 Epub Date: 2025-01-27 DOI: 10.1089/crispr.2025.0003

Bethany K Redel, Kiho Lee

引用次数: 0

Enhancements of the CRISPR-Cas System in the Silkworm Bombyx mori. 家蚕CRISPR-Cas系统的增强。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-04-01 Epub Date: 2025-03-27 DOI: 10.1089/crispr.2024.0089

Takuya Tsubota, Yoko Takasu, Naoyuki Yonemura, Hideki Sezutsu

{"title":"Enhancements of the CRISPR-Cas System in the Silkworm Bombyx mori.","authors":"Takuya Tsubota, Yoko Takasu, Naoyuki Yonemura, Hideki Sezutsu","doi":"10.1089/crispr.2024.0089","DOIUrl":"10.1089/crispr.2024.0089","url":null,"abstract":"The silkworm (Bombyx mori) is a lepidopteran model insect that has been utilized for basic research and industrial applications. In this species, transcription activator-like effector nucleases (TALENs) have been found to function efficiently, and we previously developed a TALEN-mediated genome editing system for knockout and knock-in experiments using plasmids and single-stranded oligodeoxynucleotides (ssODNs) as donors. By contrast, clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated genome editing, especially for gene integration, remains limited. In this study, we attempted to improve CRISPR-Cas systems to expand the utility of genome editing in the silkworm. Codon optimization of Cas9 improved genome editing efficiency, and single-guide RNA utilization also resulted in a higher genome editing efficiency than crRNA/tracrRNA when Cas9 messenger RNA (mRNA) was used. CRISPR-Cas12a-mediated genome editing and targeted sequence integration using ssODNs were both successfully performed. Overall, our study provides a robust technical platform that can facilitate basic and applied silkworm studies.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"155-164"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732842","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

An Overview and Comparative Analysis of CRISPR-SpCas9 gRNA Activity Prediction Tools. CRISPR-SpCas9 gRNA活性预测工具综述及比较分析

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-04-01 Epub Date: 2025-03-27 DOI: 10.1089/crispr.2024.0058

Hao Yuan, Chunping Song, Huixin Xu, Ying Sun, Christian Anthon, Lars Bolund, Lin Lin, Karim Benabdellah, Ciaran Lee, Yong Hou, Jan Gorodkin, Yonglun Luo

{"title":"An Overview and Comparative Analysis of CRISPR-SpCas9 gRNA Activity Prediction Tools.","authors":"Hao Yuan, Chunping Song, Huixin Xu, Ying Sun, Christian Anthon, Lars Bolund, Lin Lin, Karim Benabdellah, Ciaran Lee, Yong Hou, Jan Gorodkin, Yonglun Luo","doi":"10.1089/crispr.2024.0058","DOIUrl":"10.1089/crispr.2024.0058","url":null,"abstract":"Design of guide RNA (gRNA) with high efficiency and specificity is vital for successful application of the CRISPR gene editing technology. Although many machine learning (ML) and deep learning (DL)-based tools have been developed to predict gRNA activities, a systematic and unbiased evaluation of their predictive performance is still needed. Here, we provide a brief overview of in silico tools for CRISPR design and assess the CRISPR datasets and statistical metrics used for evaluating model performance. We benchmark seven ML and DL-based CRISPR-Cas9 editing efficiency prediction tools across nine CRISPR datasets covering six cell types and three species. The DL models CRISPRon and DeepHF outperform the other models exhibiting greater accuracy and higher Spearman correlation coefficient across multiple datasets. We compile all CRISPR datasets and in silico prediction tools into a GuideNet resource web portal, aiming to facilitate and streamline the sharing of CRISPR datasets. Furthermore, we summarize features affecting CRISPR gene editing activity, providing important insights into model performance and the further development of more accurate CRISPR prediction models.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"89-104"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732784","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

Exploring the Cytoplasmic Retention of CRISPR-Cas9 in Eukaryotic Cells: The Role of Nuclear Localization Signals and Ribosomal Interactions. 探索真核细胞中CRISPR-Cas9的细胞质保留：核定位信号和核糖体相互作用的作用。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-04-01 Epub Date: 2025-02-28 DOI: 10.1089/crispr.2024.0074

Rami M Major, Christine A Mills, Lei Xing, James L Krantz, Justin M Wolter, Mark J Zylka

{"title":"Exploring the Cytoplasmic Retention of CRISPR-Cas9 in Eukaryotic Cells: The Role of Nuclear Localization Signals and Ribosomal Interactions.","authors":"Rami M Major, Christine A Mills, Lei Xing, James L Krantz, Justin M Wolter, Mark J Zylka","doi":"10.1089/crispr.2024.0074","DOIUrl":"10.1089/crispr.2024.0074","url":null,"abstract":"Cas9 must be localized to the nucleus to access the genome of mammalian cells. For most proteins, adding a single nuclear localization signal (NLS) is sufficient to promote nuclear entry. However, Cas9 nuclear entry appears to be inefficient as multiple NLSs are typically added to Cas9. Here, we found that three different Cas9 variants interact with the ribosome in HEK293T cells, and that this interaction is RNA mediated. Following immunoprecipitation-mass spectrometry of cytoplasmic-localized Cas9-0NLS and nuclear-localized Cas9-4NLS constructs, we identified novel Cas9 interactors in postmitotic neurons, including KEAP1 and additional ribosomal subunits, the latter were enriched in Cas9-0NLS samples. Collectively, our results suggest that Cas9 is sequestered in the cytoplasm of mammalian cells, in part, via interaction with the ribosome. Increasing the number of NLSs on Cas9 and/or increasing the amount of cytoplasmic guide RNA has the potential to outcompete ribosomal RNA binding and promote efficient nuclear localization of CRISPR-Cas9 variants.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"120-136"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143528006","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

Genome Editing Headwinds: Can CRISPR Stay on Target? 基因组编辑的逆风：CRISPR 能否保持目标？

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-04-01 Epub Date: 2025-03-27 DOI: 10.1089/crispr.2025.0024

Rodolphe Barrangou

引用次数: 0

Re: Novel Off-Targeting Events Identified after Genome-Wide Analysis of CRISPR-Cas Edited Pigs. 对CRISPR-Cas编辑的猪进行全基因组分析后发现了新的脱靶事件。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-04-01 Epub Date: 2025-02-28 DOI: 10.1089/crispr.2024.0091

Ashley L Cook, Adam L Moyer, Lynne Boxer, Alexis L Norris

引用次数: 0

Acknowledgment of Reviewers 2024. 审稿人致谢

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

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

Managing Expectations for CRISPR in a Volatile World. 在动荡的世界中管理对CRISPR的期望。

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. 监测陆地和海洋：通过CRISPR-Cas驱动的环境DNA枯竭和富集提高效率。

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":"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