CRISPR Journal最新文献_第4页

Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems. V型CRISPR系统的12个新亚型和变体的初步表征

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-04-01 Epub Date: 2025-03-31 DOI: 10.1089/crispr.2024.0100

Jesse Tordoff, Lauren E Alfonse, Kira S Makarova, Alexa Ornstein, Anthony J Garrity, Winston X Yan, David A Scott, Eugene V Koonin, David R Cheng

{"title":"Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems.","authors":"Jesse Tordoff, Lauren E Alfonse, Kira S Makarova, Alexa Ornstein, Anthony J Garrity, Winston X Yan, David A Scott, Eugene V Koonin, David R Cheng","doi":"10.1089/crispr.2024.0100","DOIUrl":"10.1089/crispr.2024.0100","url":null,"abstract":"Type V CRISPR systems are highly diverse in sequence, mechanism, and function. Although recent efforts have greatly expanded our understanding of their evolution, the diversity of type V systems remains to be completely explored, and many clades have not been experimentally characterized. In this work, we mined metagenomic databases to identify three new subtypes and nine new variants of Cas12, the effector of Type V systems, and provide experimental and computational characterization of their Protospacer-Adjacent Motif (PAM), interference activity, loci architecture, and tracrRNA dependence. Half of the new Cas12s are found in phages or prophages. New subtypes Cas12o and Cas12p lack the canonical RuvC catalytic residues, suggesting they interfere with the target without cleavage, possibly by blocking transcription or replication. One variant, Cas12f10, displays substantial activity on PAM-less targets. Our work expands the diversity of the functionally characterized Cas12 effectors and provides some promising candidates for genome engineering tools.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"149-154"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12171694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Strategies for Interdisciplinary Human Gene Editing Research: Insights from a Swiss Project. 跨学科人类基因编辑研究的策略：来自瑞士项目的见解。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-04-01 Epub Date: 2025-04-02 DOI: 10.1089/crispr.2024.0041

Agnes Kandlbinder, Marie-Hélène Peter-Spiess, Brigitte Leeners, Amina Mollaysa, Tommaso Cavazza, Anina Meier, Michael Braunschweig, Eleonora Ioannidi, Gerald Schwank, Michael Krauthammer

{"title":"Strategies for Interdisciplinary Human Gene Editing Research: Insights from a Swiss Project.","authors":"Agnes Kandlbinder, Marie-Hélène Peter-Spiess, Brigitte Leeners, Amina Mollaysa, Tommaso Cavazza, Anina Meier, Michael Braunschweig, Eleonora Ioannidi, Gerald Schwank, Michael Krauthammer","doi":"10.1089/crispr.2024.0041","DOIUrl":"10.1089/crispr.2024.0041","url":null,"abstract":"CRISPR gene editing is a cutting-edge technology that has advanced tremendously in recent years. The first clinical CRISPR applications have been approved, and more gene editing therapies are to be expected in human medicine. Consequently, continuous basic research is needed to assess possibilities and prime future clinical applications. Because this technology not only offers new possibilities for treating diseases but also raises important ethical and societal questions, collaboration between human, life, biomedical, and medical sciences is needed. In this article, we discuss the practical challenges of such interdisciplinary projects and present strategies for addressing them based on our experience of conducting an interdisciplinary project on CRISPR. This work aims to help and encourage interdisciplinary collaborations and discussions on modern scientific endeavors that, such as gene editing, tend to blur the lines between traditional disciplines. The strategies suggested include realistic expectations, shared goals, space setting, and expert and lay dialogue.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"79-88"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143774789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hairpin Internal Nuclear Localization Signals in CRISPR-Cas9 Enhance Editing in Primary Human Lymphocytes. CRISPR-Cas9中的发夹内核定位信号增强了人原代淋巴细胞的编辑作用。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-04-01 Epub Date: 2025-03-31 DOI: 10.1089/crispr.2024.0080

Eric A Noel, Srishti U Sahu, Stacia K Wyman, Netravathi Krishnappa, Chris Jeans, Ross C Wilson

{"title":"Hairpin Internal Nuclear Localization Signals in CRISPR-Cas9 Enhance Editing in Primary Human Lymphocytes.","authors":"Eric A Noel, Srishti U Sahu, Stacia K Wyman, Netravathi Krishnappa, Chris Jeans, Ross C Wilson","doi":"10.1089/crispr.2024.0080","DOIUrl":"10.1089/crispr.2024.0080","url":null,"abstract":"The incorporation of nuclear localization signal (NLS) sequences at one or both termini of CRISPR enzymes is a widely adopted strategy to facilitate genome editing. Engineered variants of CRISPR enzymes with diverse NLS sequences have demonstrated superior performance, promoting nuclear localization and efficient DNA editing. However, limiting NLS fusion to the CRISPR protein's termini can negatively impact protein yield via recombinant expression. Here we present a distinct strategy involving the installation of hairpin internal NLS sequences (hiNLS) at rationally selected sites within the backbone of CRISPR-Cas9. We evaluated the performance of these hiNLS Cas9 variants by editing genes in human primary T cells following the delivery of ribonucleoprotein enzymes via either electroporation or co-incubation with amphiphilic peptides. We show that hiNLS Cas9 variants can improve editing efficiency in T cells compared with constructs with terminally fused NLS sequences. Furthermore, many hiNLS Cas9 constructs can be produced with high purity and yield, even when these constructs contain as many as nine NLS. These hiNLS Cas9 constructs represent a key advance in optimizing CRISPR effector design and may contribute to improved editing outcomes in research and therapeutic applications.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"105-119"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755330","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 : 2025-04-01 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