全基因组CRISPR引导RNA设计及GuideScan2特异性分析

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-02-26 DOI:10.1186/s13059-025-03488-8

Henri Schmidt, Minsi Zhang, Dimitar Chakarov, Vineet Bansal, Haralambos Mourelatos, Francisco J. Sánchez-Rivera, Scott W. Lowe, Andrea Ventura, Christina S. Leslie, Yuri Pritykin

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引用次数: 0

摘要

我们提出了GuideScan2，用于内存高效，可并行构建高特异性CRISPR引导RNA （gRNA）数据库，以及针对定制基因组中的编码区和非编码区设计和分析单个gRNA和gRNA库。GuideScan2分析在已发表的CRISPR筛选中确定了低特异性gRNA的广泛混淆效应，并使gRNA文库的构建能够减少基因本质筛选中的脱靶效应。GuideScan2还可以在杂交小鼠基因组中设计和实验验证等位基因特异性grna。GuideScan2将促进CRISPR实验的广泛应用。

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Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2

We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA libraries for targeting coding and non-coding regions in custom genomes. GuideScan2 analysis identifies widespread confounding effects of low-specificity gRNAs in published CRISPR screens and enables construction of a gRNA library that reduces off-target effects in a gene essentiality screen. GuideScan2 also enables the design and experimental validation of allele-specific gRNAs in a hybrid mouse genome. GuideScan2 will facilitate CRISPR experiments across a wide range of applications.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.