Secondary structure RNA elements control the cleavage activity of DICER

Trung Duc Nguyen, Tam Anh Trinh, Sheng Bao and Tuan Anh Nguyen ()
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Trung Duc Nguyen: The Hong Kong University of Science and Technology
Tam Anh Trinh: The Hong Kong University of Science and Technology
Sheng Bao: The Hong Kong University of Science and Technology
Tuan Anh Nguyen: The Hong Kong University of Science and Technology

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract The accurate and efficient cleavage of shRNAs and pre-miRNAs by DICER is crucial for their gene-silencing activity. Here, we conduct high-throughput DICER cleavage assays for more than ~20,000 different shRNAs and show the comprehensive cleavage activities of DICER on these sequences. We discover a single-nucleotide bulge (22-bulge), which facilitates the cleavage activity of DICER on shRNAs and human pre-miRNAs. As a result, this 22-bulge enhances the gene-silencing activity of shRNAs and the accuracy of miRNA biogenesis. In addition, various single-nucleotide polymorphism-edited 22-bulges are found to govern the cleavage sites of DICER on pre-miRNAs and thereby control their functions. Finally, we identify the single cleavage of DICER and reveal its molecular mechanism. Our findings improve the understanding of the DICER cleavage mechanism, provide a foundation for the design of accurate and efficient shRNAs for gene-silencing, and indicate the function of bulges in regulating miRNA biogenesis.

Date: 2022
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DOI: 10.1038/s41467-022-29822-3

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