CRISPR-Assisted Detection of RNA-Protein Interactions in Living Cells

Yi, Wenkai; Li, Jingyu; Zhu, Xiaoxuan; Wang, Xi; Fan, Ligang; Sun, Wen‐Hua; Liao, Linbu; Zhang, Jilin; Li, Xiaoyü; Ye, Jing; Chen, Fulin; Taipale, Jussi; Chan, Kui Ming; Zhang, Liang; Yan, Jian

doi:10.21203/rs.3.pex-904/v1

Cited by 10 publications

(9 citation statements)

References 4 publications

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“…Recently, using CRISPR/ CasRx-based RNA targeting and proximity labeling to characterize specific long non-coding RNAs (lncRNAs) binding proteins in primary cells, Yi et al established the CRISPR-assisted RNA-protein interaction detection method (CARPID). The detection method was applied in nuclear lncRNA XIST and captured a range of known interacting proteins and plentiful unidentified binding proteins [186]. This tool can be used to detect the RNAbinding proteins that are significantly involved in tumorigenesis, and these protein molecules may serve as drug targets for treating tumor-related diseases.…”

Section: Application Of Crispr/cas System In a New Emerging Hotspot Of Oncologymentioning

confidence: 99%

Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer

et al. 2021

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The 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for the development of the Clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease9 (CRISPR/Cas9) gene editing technology that provided new tools for precise gene editing. It is possible to target any genomic locus virtually using only a complex nuclease protein with short RNA as a site-specific endonuclease. Since cancer is caused by genomic changes in tumor cells, CRISPR/Cas9 can be used in the field of cancer research to edit genomes for exploration of the mechanisms of tumorigenesis and development. In recent years, the CRISPR/Cas9 system has been increasingly used in cancer research and treatment and remarkable results have been achieved. In this review, we introduced the mechanism and development of the CRISPR/Cas9-based gene editing system. Furthermore, we summarized current applications of this technique for basic research, diagnosis and therapy of cancer. Moreover, the potential applications of CRISPR/Cas9 in new emerging hotspots of oncology research were discussed, and the challenges and future directions were highlighted.

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Section: Application Of Crispr/cas System In a New Emerging Hotspot Of Oncologymentioning

confidence: 99%

Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer

et al. 2021

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“…Similar to the RPL technique, CRUIS relies on the enrichment of the labeled proteins and mass spectrometry (Ziheng Zhang, Sun, et al, 2020). Finally, a method called CAPRID (CRISPR–CasRx‐based RNA targeting and proximity labeling) was developed to identify proteins binding to specific nuclear lncRNAs in mouse cells (Yi et al, 2020). The advantage of all of these methods is that they allow mapping RNA–protein interactions in the native cellular environment; moreover, they require neither cross‐linking nor any genomic manipulation of the genes encoding the RNA of interest.…”

Section: Cas13 Applicationsmentioning

confidence: 99%

Applications of the versatile CRISPR‐Cas13 RNA targeting system

Kordyś

Sen²,

Warkocki³

2021

WIREs RNA

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CRISPR-Cas are adaptable natural prokaryotic defense systems that act against invading viruses and plasmids. Among the six currently known major CRISPR-Cas types, the type VI CRISPR-Cas13 is the only one known to exclusively bind and cleave foreign RNA. Within the last couple of years, this system has been adapted to serve numerous, and sometimes not obvious, applications, including some that might be developed as effective molecular therapies. Indeed, Cas13 has been adapted to kill antibiotic-resistant bacteria. In a cellfree environment, Cas13 has been used in the development of highly specific, sensitive, multiplexing-capable, and field-adaptable detection tools. Importantly, Cas13 can be reprogrammed and applied to eukaryotes to either combat pathogenic RNA viruses or in the regulation of gene expression, facilitating the knockdown of mRNA, circular RNA, and noncoding RNA. Furthermore, Cas13 has been harnessed for in vivo RNA modifications including programmable regulation of alternative splicing, A-to-I and C to U editing, and m6A modifications. Finally, approaches allowing for the detection and characterization of RNA-interacting proteins have also been demonstrated. Here, we provide a comprehensive overview of the applications utilizing CRISPR-Cas13 that illustrate its versatility. We also discuss the most important limitations of the CRISPR-Cas13-based technologies, and controversies regarding them. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications K E Y W O R D S bactericidal agents, CRISPR-Cas13, gene knockdown, RNA editing, RNA methods | INTRODUCTIONOver the last three decades, several seminal discoveries not only advanced general knowledge of RNA and RNA metabolism in living organisms and viruses, but also they led to the development of RNA-targeted molecular tools. These have opened up new opportunities for scientific and therapeutic applications. The big breakthrough at the turn of this

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“…In other words, lncRNAs can alleviate the repressive effect of miRNAs on mRNA expression by adsorbing miRNAs as sponges (9). In addition, lncRNAs can also interact with RNA-binding proteins (10). lncRNAs in the nucleus may be involved in the transcriptional regulation of genes (11).…”

Section: Introductionmentioning

confidence: 99%

lncKRT16P6 promotes tongue squamous cell carcinoma progression by sponging miR‑3180 and regulating GATAD2A expression

Zhang

Wang

et al. 2022

Int J Oncol

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Tongue squamous cell carcinoma (TSCC) is characterized by a poor prognosis and its 5-year overall survival rate has not improved significantly. However, the precise molecular mechanisms underlying TSCC remain largely unknown. Through RNA screening, the present study identified a novel long noncoding RNA (lncRNA), keratin 16 pseudogene 6 (lncKRT16P6), which was upregulated in TSCC tissues and cell lines and associated with TSCC tumor stage and differentiation grade. Inhibition of lncKRT16P6 expression reduced TSCC cell migration, invasion and proliferation. lncKRT16P6 sponged microRNA (miR)-3180 and upregulated GATA zinc finger domain containing 2A (GATAD2A) expression. miR-3180 inhibition reversed the lncKRT16P6 depletion-induced attenuation of TSCC malignancy and GATAD2A depletion reversed the miR-3180 silencing-induced enhancement of TSCC malignancy. In summary, the present study revealed a potential competitive endogenous RNA (ceRNA) regulatory pathway in which lncKRT16P6 modulates GATAD2A expression by binding miR-3180, ultimately promoting tumorigenesis and metastasis in TSCC. Therefore, lncKRT16P6 may be used as a prognostic biomarker and therapeutic target for clinical intervention in TSCC.

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CRISPR-Assisted Detection of RNA-Protein Interactions in Living Cells

Cited by 10 publications

References 4 publications

Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer

Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer

Applications of the versatile CRISPR‐Cas13 RNA targeting system

lncKRT16P6 promotes tongue squamous cell carcinoma progression by sponging miR‑3180 and regulating GATAD2A expression

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