Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1

Hamed Kooshapur,Carlo Camilloni,Frank Gabel,Javier F Caceres,Gracjan Michlewski,Andre Dallmann,Alexander Jussupow,Alisha N Jones,Michael Sattler,Noemi Fernandez,Nila Roy Choudhury,Bernd Simon,Max Mühlbauer

doi:10.1038/s41467-018-04871-9

Abstract

Post-transcriptional mechanisms play a predominant role in the control of microRNA (miRNA) production. Recognition of the terminal loop of precursor miRNAs by RNA-binding proteins (RBPs) influences their processing; however, the mechanistic basis for how levels of individual or subsets of miRNAs are regulated is mostly unexplored. We previously showed that hnRNP A1, an RBP implicated in many aspects of RNA processing, acts as an auxiliary factor that promotes the Microprocessor-mediated processing of pri-mir-18a. Here, by using an integrative structural biology approach, we show that hnRNP A1 forms a 1:1 complex with pri-mir-18a where both RNA recognition motifs (RRMs) bind to cognate RNA sequence motifs in the terminal loop of pri-mir-18a. Terminal loop binding induces an allosteric destabilization of base-pairing in the pri-mir-18a stem that promotes its downstream processing. Our results highlight terminal loop RNA recognition by RBPs as a potential general principle of miRNA biogenesis and regulation.

Highlights

Post-transcriptional mechanisms play a predominant role in the control of microRNA production
To identify which regions in hnRNP A1 are required for stimulating pri-mir-18a processing in living cells we used an in vivo processing assay
We found that overexpression of fulllength hnRNP A1 results in a ~two-fold increase in the levels of mature miR-18a, whereas UP1, comprising both RNA recognition motifs (RRMs) but lacking the M9 sequence, has no effect—due to its cytoplasmic localization (Fig. 1c; Supplementary Fig. 1a, b; Supplementary Table 1)

Summary

Introduction

Post-transcriptional mechanisms play a predominant role in the control of microRNA (miRNA) production. MicroRNAs (miRNAs, miRs) are a class of highly conserved small non-coding RNAs that play a crucial role in the regulation of gene expression. They are involved in a variety of biological processes including cell growth, proliferation, and differentiation[1]. Binding to the terminal loop induces an allosteric destabilization of base-pairing in the pri-mir-18a stem that promote its processing.

Methods

Results

Conclusion