CRISPR Journal最新文献_第7页

Discovery and Characterization of Novel Type V Cas12f Nucleases with Diverse Protospacer Adjacent Motif Preferences. 具有不同原间隔基序邻近基序偏好的新型V型Cas12f核酸酶的发现和表征

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.0006

Allison Sharrar, Luisa Arake de Tacca, Trevor Collingwood, Zuriah Meacham, David Rabuka, Johanna Staples-Ager, Michael Schelle

{"title":"Discovery and Characterization of Novel Type V Cas12f Nucleases with Diverse Protospacer Adjacent Motif Preferences.","authors":"Allison Sharrar, Luisa Arake de Tacca, Trevor Collingwood, Zuriah Meacham, David Rabuka, Johanna Staples-Ager, Michael Schelle","doi":"10.1089/crispr.2023.0006","DOIUrl":"https://doi.org/10.1089/crispr.2023.0006","url":null,"abstract":"Small Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) effectors are key to developing gene editing therapies due to the packaging constraints of viral vectors. While Cas9 and Cas12a CRISPR-Cas effectors have advanced into select clinical applications, their size is prohibitive for efficient delivery of both nuclease and guide RNA in a single viral vector. Type V Cas12f effectors present a solution given their small size. In this study, we describe a novel set of miniature (<490AA) Cas12f nucleases that cleave double-stranded DNA in human cells. We determined their optimal trans-activating RNA empirically through rational modifications, which resulted in an optimal single guide RNA. We show that these nucleases have broad protospacer adjacent motif (PAM) preferences, allowing for expanded genome targeting. The unique characteristics of these novel nucleases add to the diversity of the miniature CRISPR-Cas toolbox while the expanded PAM allows for the editing of genomic locations that could not be accessed with existing Cas12f nucleases.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10037354","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: 1

Predicting Mutations Generated by Cas9, Base Editing, and Prime Editing in Mammalian Cells. 预测哺乳动物细胞中Cas9、碱基编辑和引体编辑产生的突变。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.0016

Juliane Weller, Ananth Pallaseni, Jonas Koeppel, Leopold Parts

引用次数: 0

Rosalind Franklin Society Proudly Announces the 2022 Award Recipient for The CRISPR Journal. 罗莎琳德·富兰克林协会自豪地宣布了2022年CRISPR杂志的获奖者。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.29162.rfs2022

Nicole F Brackett

引用次数: 0

Fanzors: Mysterious TnpB-Like Bacterial Transposon-Related RNA-Guided DNA Nucleases of Eukaryotes. 神秘的tnpb样细菌转座子相关rna引导的真核生物DNA核酸酶。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.29164.tka

Tautvydas Karvelis, Virginijus Siksnys

引用次数: 0

CRISPR Milestones for Sustainable Agriculture and Forestry. 可持续农业和林业的CRISPR里程碑。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.29163.editorial

Rodolphe Barrangou

引用次数: 0

Multiplex Editing of the Nucleoredoxin1 Tandem Array in Poplar: From Small Indels to Translocations and Complex Inversions. 杨树核还原蛋白1串联阵列的多重编辑:从小索引到易位和复杂反转。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2022.0096

Yen-Ho Chen, Shakuntala Sharma, William P Bewg, Liang-Jiao Xue, Cole R Gizelbach, Chung-Jui Tsai

{"title":"Multiplex Editing of the Nucleoredoxin1 Tandem Array in Poplar: From Small Indels to Translocations and Complex Inversions.","authors":"Yen-Ho Chen, Shakuntala Sharma, William P Bewg, Liang-Jiao Xue, Cole R Gizelbach, Chung-Jui Tsai","doi":"10.1089/crispr.2022.0096","DOIUrl":"https://doi.org/10.1089/crispr.2022.0096","url":null,"abstract":"The CRISPR-Cas9 system has been deployed for precision mutagenesis in an ever-growing number of species, including agricultural crops and forest trees. Its application to closely linked genes with extremely high sequence similarities has been less explored. In this study, we used CRISPR-Cas9 to mutagenize a tandem array of seven Nucleoredoxin1 (NRX1) genes spanning ∼100 kb in Populus tremula × Populus alba. We demonstrated efficient multiplex editing with one single guide RNA in 42 transgenic lines. The mutation profiles ranged from small insertions and deletions and local deletions in individual genes to large genomic dropouts and rearrangements spanning tandem genes. We also detected complex rearrangements including translocations and inversions resulting from multiple cleavage and repair events. Target capture sequencing was instrumental for unbiased assessments of repair outcomes to reconstruct unusual mutant alleles. The work highlights the power of CRISPR-Cas9 for multiplex editing of tandemly duplicated genes to generate diverse mutants with structural and copy number variations to aid future functional characterization.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10460964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10100491","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

Rapid and Technically Simple Detection of SARS-CoV-2 Variants Using CRISPR Cas12 and Cas13. 利用CRISPR Cas12和Cas13快速、技术简单地检测SARS-CoV-2变体

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.0007

Gabriel Lamothe, Julie Carbonneau, Charles Joly Beauparlant, Thierry Vincent, Patrik Quessy, Anthony Guedon, Gary Kobinger, Jean-Francois Lemay, Guy Boivin, Arnaud Droit, Nathalie Turgeon, Jacques P Tremblay

{"title":"Rapid and Technically Simple Detection of SARS-CoV-2 Variants Using CRISPR Cas12 and Cas13.","authors":"Gabriel Lamothe, Julie Carbonneau, Charles Joly Beauparlant, Thierry Vincent, Patrik Quessy, Anthony Guedon, Gary Kobinger, Jean-Francois Lemay, Guy Boivin, Arnaud Droit, Nathalie Turgeon, Jacques P Tremblay","doi":"10.1089/crispr.2023.0007","DOIUrl":"https://doi.org/10.1089/crispr.2023.0007","url":null,"abstract":"The worldwide proliferation of the SARS-CoV-2 virus in the past 3 years has allowed the virus to accumulate numerous mutations. Dangerous lineages have emerged one after another, each leading to a new wave of the pandemic. In this study, we have developed the THRASOS pipeline to rapidly discover lineage-specific mutation signatures and thus advise the development of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based diagnostic tests. We also optimized a strategy to modify loop-mediated isothermal amplification amplicons for downstream use with Cas12 and Cas13 for future multiplexing. The close ancestry of the BA.1 and BA.2 variants of SARS-CoV-2 (Omicron) made these excellent candidates for the development of a first test using this workflow. With a quick turnaround time and low requirements for laboratory equipment, the test we have created is ideally suited for settings such as mobile clinics lacking equipment such as Next-Generation Sequencers or Sanger Sequencers and the personnel to run these devices.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10027205","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-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning. 基于CRISPR- cas的海洋环境生物监测:通过深度学习实现CRISPR RNA设计优化。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.0019

Benjamín Durán-Vinet, Karla Araya-Castro, Anastasija Zaiko, Xavier Pochon, Susanna A Wood, Jo-Ann L Stanton, Gert-Jan Jeunen, Michelle Scriver, Anya Kardailsky, Tzu-Chiao Chao, Deependra K Ban, Maryam Moarefian, Kiana Aran, Neil J Gemmell

{"title":"CRISPR-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning.","authors":"Benjamín Durán-Vinet, Karla Araya-Castro, Anastasija Zaiko, Xavier Pochon, Susanna A Wood, Jo-Ann L Stanton, Gert-Jan Jeunen, Michelle Scriver, Anya Kardailsky, Tzu-Chiao Chao, Deependra K Ban, Maryam Moarefian, Kiana Aran, Neil J Gemmell","doi":"10.1089/crispr.2023.0019","DOIUrl":"https://doi.org/10.1089/crispr.2023.0019","url":null,"abstract":"Almost all of Earth's oceans are now impacted by multiple anthropogenic stressors, including the spread of nonindigenous species, harmful algal blooms, and pathogens. Early detection is critical to manage these stressors effectively and to protect marine systems and the ecosystem services they provide. Molecular tools have emerged as a promising solution for marine biomonitoring. One of the latest advancements involves utilizing CRISPR-Cas technology to build programmable, rapid, ultrasensitive, and specific diagnostics. CRISPR-based diagnostics (CRISPR-Dx) has the potential to allow robust, reliable, and cost-effective biomonitoring in near real time. However, several challenges must be overcome before CRISPR-Dx can be established as a mainstream tool for marine biomonitoring. A critical unmet challenge is the need to design, optimize, and experimentally validate CRISPR-Dx assays. Artificial intelligence has recently been presented as a potential approach to tackle this challenge. This perspective synthesizes recent advances in CRISPR-Dx and machine learning modeling approaches, showcasing CRISPR-Dx potential to progress as a rising molecular tool candidate for marine biomonitoring applications.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10494903/pdf/crispr.2023.0019.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10220671","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

CRISPR and the Plant Pathologists' Holy Grail. CRISPR和植物病理学家的圣杯。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.29165.mwi

Matthew R Willmann

引用次数: 0

CRISPR Comparison Toolkit: Rapid Identification, Visualization, and Analysis of CRISPR Array Diversity. CRISPR比较工具箱:快速鉴定，可视化和分析CRISPR阵列多样性。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2022.0080

Alan J Collins, Rachel J Whitaker

引用次数: 4