Screening for functional circular RNAs using the CRISPR–Cas13 system

Li, Siqi; Li, Xiang; Xue, Wei; Zhang, Lin; Yang, Liang-Zhong; Cao, Shi-Meng; Lei, Yun-Ni; Liu, Chu-Xiao; Guo, Si-Kun; Shan, Lin; Wu, Man; Tao, Xiao; Zhang, Jialin; Gao, Xiang; Zhang, Jun; Wei, Jia; Li, Jinsong; Yang, Li; Chen, Lingling

doi:10.1038/s41592-020-01011-4

Cited by 218 publications

(161 citation statements)

References 41 publications

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“…The knockdown efficiency of all available Cas13 family proteins (LwaCas13a, PguCas13b, PspCas13b, RanCas13b, AdmCas13d, EsCas13d, or RfxCas13d) were compared for circPOLR2A and circRTN4 in vitro. 35 Most of them could knockdown the circRNAs with no detectable effects on their linear counterparts, but RfxCas13d exhibited the highest knockdown efficiency. RfxCas13d was used to target many other circRNAs, and results showed specific and robust knockdown of all circRNAs.…”

Section: Strategies To Target Circrnasmentioning

confidence: 99%

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Targeting circular RNAs as a therapeutic approach: current strategies and challenges

Liu

et al. 2021

Sig Transduct Target Ther

294

216

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Significant progress has been made in circular RNA (circRNA) research in recent years. Increasing evidence suggests that circRNAs play important roles in many cellular processes, and their dysregulation is implicated in the pathogenesis of various diseases. CircRNAs are highly stable and usually expressed in a tissue- or cell type-specific manner. Therefore, they are currently being explored as potential therapeutic targets. Gain-of-function and loss-of-function approaches are typically performed using circRNA expression plasmids and RNA interference-based strategies, respectively. These strategies have limitations that can be mitigated using nanoparticle and exosome delivery systems. Furthermore, recent developments show that the cre-lox system can be used to knockdown circRNAs in a cell-specific manner. While still in the early stages of development, the CRISPR/Cas13 system has shown promise in knocking down circRNAs with high specificity and efficiency. In this review, we describe circRNA properties and functions and highlight their significance in disease. We summarize strategies that can be used to overexpress or knockdown circRNAs as a therapeutic approach. Lastly, we discuss major challenges and propose future directions for the development of circRNA-based therapeutics.

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Section: Strategies To Target Circrnasmentioning

confidence: 99%

“… 33 , 34 Furthermore, CRISPR technology and Cas13 systems in particular have demonstrated great potential in knocking down circRNAs in a specific and robust manner. 35 , 36 …”

Section: Introductionmentioning

confidence: 99%

Targeting circular RNAs as a therapeutic approach: current strategies and challenges

Liu

et al. 2021

Sig Transduct Target Ther

294

216

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“…METLIN MS2, is chemical standards spectral DB that is well annotated and structurally diverse database consisting of over 850,000 chemical standards with MS/MS data generated in both positive and negative ionization modes at multiple collision energies (CEs), collectively containing over 4,000,000 curated HR MS/MS data that covers almost 1% of PubChem’s 93 million compounds (Xue et al 2020 ).…”

Section: Databasesmentioning

confidence: 99%

New software tools, databases, and resources in metabolomics: updates from 2020

Misra

2021

Metabolomics

136

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Background Precision medicine, space exploration, drug discovery to characterization of dark chemical space of habitats and organisms, metabolomics takes a centre stage in providing answers to diverse biological, biomedical, and environmental questions. With technological advances in mass-spectrometry and spectroscopy platforms that aid in generation of information rich datasets that are complex big-data, data analytics tend to co-evolve to match the pace of analytical instrumentation. Software tools, resources, databases, and solutions help in harnessing the concealed information in the generated data for eventual translational success. Aim of the review In this review, ~ 85 metabolomics software resources, packages, tools, databases, and other utilities that appeared in 2020 are introduced to the research community. Key scientific concepts of review In Table 1 the computational dependencies and downloadable links of the tools are provided, and the resources are categorized based on their utility. The review aims to keep the community of metabolomics researchers updated with all the resources developed in 2020 at a collated avenue, in line with efforts form 2015 onwards to help them find these at one place for further referencing and use.

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“…There is no standard nomenclature of circRNAs, although the study of circRNAs has exploded in the past few years, which is not convenient for academic exchanges (155). Many individual circRNA functions remain unknown due to the lack of adequate methods for distinguishing circRNAs from cognate mRNAs with overlapping exons (156). RNA sequencing (RNA-seq) data are used to detect genome-wide circRNA expression by numerous algorithms, but there is no clear standard way to evaluate the accuracy of these algorithms and little overlap in their predictions (157).…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Insights Into the Involvement of Circular RNAs in Autoimmune Diseases

et al. 2021

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Circular RNAs (circRNAs) are single-stranded, endogenous, non-coding RNA (ncRNA) molecules formed by the backsplicing of messenger RNA (mRNA) precursors and have covalently closed circular structures without 5′-end caps and 3′-end polyadenylation [poly(A)] tails. CircRNAs are characterized by abundant species, stable structures, conserved sequences, cell- or tissue-specific expression, and widespread and stable presence in many organisms. Therefore, circRNAs can be used as biomarkers for the prediction, diagnosis, and treatment of a variety of diseases. Autoimmune diseases (AIDs) are caused by defects in immune tolerance or abnormal immune regulation, which leads to damage to host organs. Due to the complexity of the pathophysiological processes of AIDs, clinical therapeutics have been suboptimal. The emergence of circRNAs sheds new light on the treatment of AIDs. In particular, circRNAs mainly participate in the occurrence and development of AIDs by sponging targets. This review systematically explains the formation, function, mechanism, and characteristics of circRNAs in the context of AIDs. With a deeper understanding of the pathophysiological functions of circRNAs in the pathogenesis of AIDs, circRNAs may become reasonable, accurate, and effective biomarkers for the diagnosis and treatment of AIDs in the future.

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Screening for functional circular RNAs using the CRISPR–Cas13 system

Cited by 218 publications

References 41 publications

Targeting circular RNAs as a therapeutic approach: current strategies and challenges

Targeting circular RNAs as a therapeutic approach: current strategies and challenges

New software tools, databases, and resources in metabolomics: updates from 2020

Insights Into the Involvement of Circular RNAs in Autoimmune Diseases

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