CRISPR Journal最新文献_第2页

Discovery of Diverse CRISPR Leader Motifs, Putative Functions, and Applications for Enhanced CRISPR Detection and Subtype Annotation. 发现多种CRISPR先导基序，推测功能，以及增强CRISPR检测和亚型注释的应用。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2025-01-08 DOI: 10.1089/crispr.2024.0093

Murat Buyukyoruk, Pushya Krishna, Andrew Santiago-Frangos, Blake Wiedenheft

{"title":"Discovery of Diverse CRISPR Leader Motifs, Putative Functions, and Applications for Enhanced CRISPR Detection and Subtype Annotation.","authors":"Murat Buyukyoruk, Pushya Krishna, Andrew Santiago-Frangos, Blake Wiedenheft","doi":"10.1089/crispr.2024.0093","DOIUrl":"10.1089/crispr.2024.0093","url":null,"abstract":"Bacteria and archaea acquire resistance to genetic parasites by preferentially integrating short fragments of foreign DNA at one end of a Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR). \"Leader\" DNA upstream of CRISPR loci regulates transcription and foreign DNA integration into the CRISPR. Here, we analyze 37,477 CRISPRs from 39,277 bacterial and 556 archaeal genomes to identify conserved sequence motifs in CRISPR leaders. A global analysis of all leader sequences fails to identify universally conserved motifs. However, an analysis of leader sequences that have been grouped by 16S rRNA-based taxonomy and CRISPR subtype reveals 87 specific motifs in type I, II, III, and V CRISPR leaders. Fourteen of these leader motifs have biochemically demonstrated roles in CRISPR biology including integration, transcription, and CRISPR RNA processing. Another 28 motifs are related to DNA binding sites for proteins with functions that are consistent with regulating CRISPR activity. In addition, we show that these leader motifs can be used to improve existing CRISPR detection methods and enhance the accuracy of CRISPR classification.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962553","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 in Apicomplexan Parasites: Current Status, Challenges, and Future Possibilities. 表皮复合寄生虫的基因组编辑：现状、挑战和未来的可能性》。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-12-01 Epub Date: 2024-10-10 DOI: 10.1089/crispr.2024.0032

Ethel Webi, Hussein M Abkallo, George Obiero, Paul Ndegwa, Shengsong Xie, Shuhong Zhao, Vishvanath Nene, Lucilla Steinaa

引用次数: 0

Correction to: Give Cas a Chance: An Actionable Path to a Platform for CRISPR Cures, by Fyodor D. Urnov [DOI: 10.1089/crispr.2024.0082]. 更正为给 Cas 一个机会：费奥多尔-D-乌尔诺夫（Fyodor D. Urnov）著：《通往 CRISPR 治疗平台的可行之路》[DOI: 10.1089/crispr.2024.0082]。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-12-01 DOI: 10.1089/crispr.2024.0082.correx

引用次数: 0

Benchmark Software and Data for Evaluating CRISPR-Cas9 Experimental Pipelines Through the Assessment of a Calibration Screen. 通过校准筛选评估 CRISPR-Cas9 实验流程的基准软件和数据。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-12-01 Epub Date: 2024-01-02 DOI: 10.1089/crispr.2023.0040

Raffaele M Iannuzzi, Ichcha Manipur, Clare Pacini, Fiona M Behan, Mario R Guarracino, Mathew J Garnett, Aurora Savino, Francesco Iorio

{"title":"Benchmark Software and Data for Evaluating CRISPR-Cas9 Experimental Pipelines Through the Assessment of a Calibration Screen.","authors":"Raffaele M Iannuzzi, Ichcha Manipur, Clare Pacini, Fiona M Behan, Mario R Guarracino, Mathew J Garnett, Aurora Savino, Francesco Iorio","doi":"10.1089/crispr.2023.0040","DOIUrl":"10.1089/crispr.2023.0040","url":null,"abstract":"Genome-wide genetic screens using CRISPR-guide RNA libraries are widely performed in mammalian cells to functionally characterize individual genes and for the discovery of new anticancer therapeutic targets. As the effectiveness of such powerful and precise tools for cancer pharmacogenomics is emerging, tools and methods for their quality assessment are becoming increasingly necessary. Here, we provide an R package and a high-quality reference data set for the assessment of novel experimental pipelines through which a single calibration experiment has been executed: a screen of the HT-29 human colorectal cancer cell line with a commercially available genome-wide library of single-guide RNAs. This package and data allow experimental researchers to benchmark their screens and produce a quality-control report, encompassing several quality and validation metrics. The R code used for processing the reference data set, for its quality assessment, as well as to evaluate the quality of a user-provided screen, and to reproduce the figures presented in this article is available at https://github.com/DepMap-Analytics/HT29benchmark. The reference data is publicly available on FigShare.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"355-365"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139075824","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

'Tis the Season: CRISPR Products All Around. 这个季节：CRISPR产品无处不在。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-12-01 Epub Date: 2024-12-06 DOI: 10.1089/crispr.2024.0094

Rodolphe Barrangou

引用次数: 0

Early Detection of Wildlife Disease Pathogens Using CRISPR-Cas System Methods. 利用 CRISPR-Cas 系统方法早期检测野生动物疾病病原体。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-12-01 Epub Date: 2024-10-31 DOI: 10.1089/crispr.2024.0030

Adam A Pérez, Guelaguetza Vazquez-Meves, Margaret E Hunter

引用次数: 0

Identification of a Guide RNA Targeting an Ultraconserved Element for Evaluation of Cas9 Genome Editors Across Mammalian Species. 鉴定靶向超保守元件的引导核糖核酸，以评估跨哺乳动物物种的 Cas9 基因组编辑器。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-12-01 Epub Date: 2024-09-23 DOI: 10.1089/crispr.2024.0053

Benjamin G Gowen, Prachi Khekare, Shannon R McCawley, Kory Melton, Craig Soares, Jean Chan, Vihasi Jani, Pierre Boivin, Ashil Bans, Weng-In Leong, Aaron J Cantor, Jack Walleshauser, Peter B Otoupal, Rina J Mepani, Adam P Silverman, Mary Haak-Frendscho, Spencer C Wei

引用次数: 0

CRISPR-GRIT: Guide RNAs with Integrated Repair Templates Enable Precise Multiplexed Genome Editing in the Diploid Fungal Pathogen Candida albicans. CRISPR-GRIT：带有集成修复模板的引导 RNA 可对二倍体真菌病原体白色念珠菌进行精确的多重基因组编辑。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-12-01 Epub Date: 2024-10-22 DOI: 10.1089/crispr.2024.0052

Christopher J Cotter, Cong T Trinh

{"title":"CRISPR-GRIT: Guide RNAs with Integrated Repair Templates Enable Precise Multiplexed Genome Editing in the Diploid Fungal Pathogen Candida albicans.","authors":"Christopher J Cotter, Cong T Trinh","doi":"10.1089/crispr.2024.0052","DOIUrl":"10.1089/crispr.2024.0052","url":null,"abstract":"Candida albicans, an opportunistic fungal pathogen, causes severe infections in immunocompromised individuals. Limited classes and overuse of current antifungals have led to the rapid emergence of antifungal resistance. Thus, there is an urgent need to understand fungal pathogen genetics to develop new antifungal strategies. Genetic manipulation of C. albicans is encumbered by its diploid chromosomes requiring editing both alleles to elucidate gene function. Although the recent development of CRISPR-Cas systems has facilitated genome editing in C. albicans, large-scale and multiplexed functional genomic studies are still hindered by the necessity of cotransforming repair templates for homozygous knockouts. Here, we present CRISPR-GRIT (Guide RNAs with Integrated Repair Templates), a repair template-integrated guide RNA design for expedited gene knockouts and multiplexed gene editing in C. albicans. We envision that this method can be used for high-throughput library screens and identification of synthetic lethal pairs in both C. albicans and other diploid organisms with strong homologous recombination machinery.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"385-394"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512851","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 Targeting of Multidrug Resistance Genes in Methicillin-Resistant Staphylococcus aureus. CRISPR-Cas9 介导的耐甲氧西林金黄色葡萄球菌多药耐药性基因靶向。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-12-01 Epub Date: 2024-11-08 DOI: 10.1089/crispr.2024.0001

Aysegul Ates, Cihan Tastan, Safak Ermertcan

{"title":"CRISPR-Cas9-Mediated Targeting of Multidrug Resistance Genes in Methicillin-Resistant Staphylococcus aureus.","authors":"Aysegul Ates, Cihan Tastan, Safak Ermertcan","doi":"10.1089/crispr.2024.0001","DOIUrl":"10.1089/crispr.2024.0001","url":null,"abstract":"Antibiotic resistance poses a global health crisis limiting the efficacy of available therapeutic agents. We explored CRISPR-Cas-based antimicrobials to combat multidrug resistance in methicillin-resistant Staphylococcus aureus (MRSA), targeting methicillin (mecA), gentamicin (aacA), and ciprofloxacin (grlA, grlB) resistance genes. Engineered CRISPR plasmids with specific single-guide RNAs were electroporated into MRSA strains. Real-time polymerase chain reaction assessed gene expression changes, while antibiotic susceptibility tests (ASTs) evaluated resistance status. Results showed a 1.5-fold decrease in mecA, a 5.5-fold decrease in grlA, a 6-fold decrease in grlB, and a 4-fold decrease in aacA expression. ASTs demonstrated the reversal of resistance to beta-lactam, quinolone, and aminoglycoside antibiotics. Western blot analysis revealed a 70% decrease in penicillin-binding protein 2a expression. Sanger sequencing confirmed point mutations in the grlB and aacA genes. Our findings highlight the potential of CRISPR-Cas9 technology to restore antibiotic efficacy against multidrug-resistant pathogens.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"374-384"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142607408","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

Engineering CjCas9 for Efficient Base Editing and Prime Editing. 对 CjCas9 进行工程改造，以实现高效的碱基编辑和基序编辑。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2024-12-01 Epub Date: 2024-11-18 DOI: 10.1089/crispr.2024.0018

Siyuan Liu, Yingdi Zhao, Qiqin Mo, Yadong Sun, Hanhui Ma

{"title":"Engineering CjCas9 for Efficient Base Editing and Prime Editing.","authors":"Siyuan Liu, Yingdi Zhao, Qiqin Mo, Yadong Sun, Hanhui Ma","doi":"10.1089/crispr.2024.0018","DOIUrl":"10.1089/crispr.2024.0018","url":null,"abstract":"The CRISPR-Cas9 system has been applied for clinical applications of gene therapy. Most CRISPR-based gene therapies are derived from Streptococcus pyogenes Cas9, which is challenging to package into a single adeno-associated virus vector and limits its clinical applications. Campylobacter jejuni Cas9 (CjCas9) is one of the smallest Cas9 proteins. CjCas9-mediated base editing (CjBE) efficiency varies across genomic sites, while CjCas9-mediated prime editing (CjPE) efficiency is less than 5% on average. Here we developed enhanced cytosine base editors (enCjCBEs) and adenine base editors (enCjABEs) by engineered CjCas9P47K. We demonstrated the robust C-to-T conversion (70% on average) by enCjCBE or A-to-G conversion (76% on average) by enCjABE. Meanwhile, we applied the CjCas9P47K variant to generate enhanced CjPE (enCjPE), which increases the editing efficiency 17-fold at the PRNP site over wild-type CjPE. Fusing nonspecific DNA binding protein Sso7d to enCjCas9 and MS2 stem-loop RNA aptamer to the 3-terminal of cognate pegRNA resulted in 12% editing efficiency on average with a 24-fold increase over wild-type CjPE, and we termed it SsenCjPE. The SsenCjPE can also be combined with hMLH1dn to further increase the editing efficiency and MMLV RTaseΔRnH to reduce size. Finally, we introduced an additional mutation D829R into SsenCjPE and generated SsenCjPE-M2 with a 61-fold increase of PE efficiency over wild-type at the PRNP site. In summary, enCjBEs, SsenCjPEs, or SsenCjPE-M2 are compact Cas9-derived BE or prime editors in biological research or biomedical applications.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":" ","pages":"395-405"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142649684","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