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CRISPRTE: A web-based tool to generate single guide RNA targets transposable elements

ABSTRACT: CRISPR/Cas systems have gained prominence as powerful tools for genome engineering. Recent investigations into the crucial role of transposable elements (TEs) have stimulated research interest in manipulating TEs to elucidate their functions. Nevertheless, designing single guide RNAs (sgRNAs) that are both specific and efficient for TE manipulation presents a formidable challenge, considering the repetitive nature and high copy numbers of TEs. Although various sgRNA design tools have been developed for gene editing, an optimized sgRNA designer explicitly for TE manipulation has yet to be established. To bridge this gap, we presented CRISPR-TE, a web-based application featuring an accessible graphical user interface, available at https://www.crisprte.cn. CRISPR-TE could identify all potential sgRNAs for TEs and offers a comprehensive solution for efficient TE targeting at both the single duplicate and subfamily levels. We also demonstrated that young TEs can be targeted with higher coverage at the subfamily level. Finally, we validated the overexpression of SVAD, a human-specific TE, using dCas9-VP64 activator incorporated with three sgRNAs designed by our tool. Collectively, our findings suggest that CRISPR-TE may serve as a versatile framework for designing sgRNAs aimed at TE targeting.

ORGANISM(S): Homo sapiens

PROVIDER: GSE228266 | GEO | 2024/03/24

REPOSITORIES: GEO

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Titrating gene expression with allelic series of CRISPR guide RNAs

Project description:Cellular phenotypes arise from the degrees to which different genes are expressed, yet the ability to monitor these phenotypes is limited by a lack of tools to precisely control gene expression. We describe the development of allelic series of systematically compromised sgRNAs to titrate expression of human genes with CRISPR interference. Using large-scale measurements of compromised sgRNA activities, we both identify empirically validated intermediate-activity sgRNAs and derive the factors governing sgRNA activity using deep learning, enabling construction of a compact sgRNA library to titrate expression of ~2,400 essential genes and a genome-wide in silico library. Staging cells along a continuum of essential gene expression levels using sgRNA series combined with rich single-cell RNA-seq readout reveals expression threshold-specific responses and gene-specific expression-to-phenotype relationships. Our work provides a general tool to control gene expression with applications ranging from tuning of biochemical pathways to identification of suppressors for diseases of dysregulated gene expression.

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Genome wide (GW) and validation CRISPR screens on encephalitogenic CD4+ T cell migration into the CNS

Project description:To identify genes driving encephalitogenic CD4+ T cell migration into the CNS, we performed a genome-wide CRISPR screen and a subsequent validation screen For the genome-wide CRISPR screen, up to 4 sgRNA per gene and 800 non targeted controls were included, for a total of 87690 individual sgRNAs, and for the validation screen, up to 6 sgRNA per gene and 241 non targeted controls for a total of 12000 individual sgRNAs

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Screening of a heptamer-type sgRNA library for therapeutic agents against hematological malignancies.

Project description:tRNase ZL-utilizing efficacious gene silencing (TRUE gene silencing) is an RNA-mediated gene expression control technology that has therapeutic potential. This technology is based on the properties of tRNase ZL that it can cleave any target RNA at any desired site under the direction of an appropriate artificial small guide RNA (sgRNA) and that cytosolic tRNase ZL can modulate gene expression by cleaving mRNA under the direction of cellular 5M-bM-^@M-2-half-tRNA or microRNA as sgRNA. In order to estimate a number of potential therapeutic heptamer-type sgRNAs for hematological malignancies, we constructed an sgRNA library composed of 156 heptamer-type sgRNAs, and examined how the sgRNAs affect viability of leukemia and myeloma cells. And we found that 20 of the 156 sgRNAs can efficiently induce apoptosis in at least one of the cancer cell lines. Furthermore, we demonstrated that 4 of the 20 effective sgRNAs can reduce growth rates of HL60 cells in mouse xenograft models. DNA microarray analysis for changes in an mRNA profile by these four heptamer-type sgRNAs suggested at least one candidate target mRNA that contains a potential tRNase ZL target site for each sgRNA. Changes in gene expression in HL60 cells were measured after 18-hour incubation in the absence or presence of one of five different heptamer-type sgRNAs. *Heptamer sequences requested but not provided by submitter

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2016-08-20 | E-GEOD-72259 | biostudies-arrayexpress

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2015-07-05 | E-GEOD-69666 | biostudies-arrayexpress

RNA-seq expression profiling of OCI-AML2 and OCI-AML3 cells upon CRISPR/Cas9 –mediated disruption of DDX3X RNA binding domain

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2019-11-23 | E-MTAB-6241 | biostudies-arrayexpress

Danio rerio

Project description:CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

| PRJNA277755 | ENA

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