Mismatched and wobble base pairs govern primary microRNA processing by human Microprocessor

Shaohua Li,Thuy Linh Nguyen,Trung Duc Nguyen,Tuan Anh Nguyen

doi:10.1038/s41467-020-15674-2

Shaohua Li, Thuy Linh Nguyen + Show 2 more

Open Access

https://doi.org/10.1038/s41467-020-15674-2

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Abstract

MicroRNAs (miRNAs) are small RNAs that regulate gene expression. miRNAs are produced from primary miRNAs (pri-miRNAs), which are cleaved by Microprocessor. Microprocessor, therefore, plays a crucial role in determining the efficiency and precision of miRNA production, and thus the function of the final miRNA product. Here, we conducted high-throughput enzymatic assays to investigate the catalytic mechanism of Microprocessor cleaving randomized pri-miRNAs. We identified multiple mismatches and wobble base pairs in the upper stem of pri-miRNAs, which influence the efficiency and accuracy of their processing. The existence of these RNA elements helps to explain the alternative cleavage of Microprocessor for some human pri-miRNAs. We also demonstrated that miRNA biogenesis can be altered via modification of the RNA elements by RNA-editing events or single nucleotide polymorphisms (SNPs). These findings improve our understanding of pri-miRNA processing mechanisms and provide a foundation for interpreting differential miRNA expression due to RNA modifications and SNPs.

Highlights

IntroductionMicroRNAs (miRNAs) are small RNAs that regulate gene expression. miRNAs are produced from primary miRNAs (pri-miRNAs), which are cleaved by Microprocessor
MicroRNAs are small RNAs that regulate gene expression. miRNAs are produced from primary miRNAs, which are cleaved by Microprocessor
We showed that the RNA elements can be modified due to RNA-editing events and single nucleotide polymorphisms (SNPs), which results in altered miRNA expression

Summary

Introduction

MicroRNAs (miRNAs) are small RNAs that regulate gene expression. miRNAs are produced from primary miRNAs (pri-miRNAs), which are cleaved by Microprocessor. DGCR8 in a dimer form plays an essential role in ensuring that DROSHA cleaves accurately ~22 nt from the apical junction This dimer interacts with the apical loop and the apical UGU motif, and in this way occupies a distinct region of the upper stem of pri-miRNA12,13,21,23. The interaction between DGCR8 and the UGU-containing apical loop is strengthened by a small molecule, called hemin[16,24] Another factor that controls the action of Microprocessor is the length of the pri-miRNA stem region[18,25]. DROSHA precisely measures the site of cleavage to be ~13 nt from the basal junction, and DGCR8 interacts with the loop and apical UGU motif located ~22 nt from the cleavage sites This means that the optimal length of the pri-miRNA stem for cleavage by Microprocessor is ~35 bp. Many pri-miRNAs exhibit various alternative cleavages, which suggests that unknown RNA elements or protein factors might influence the choice of cleavage sites by Microprocessor

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