The Drosophila Helicase MLE Targets Hairpin Structures in Genomic Transcripts.

Simona Cugusi,Peng Jin,Yujing Li,John C Lucchesi

doi:10.1371/journal.pgen.1005761

Abstract

RNA hairpins are a common type of secondary structures that play a role in every aspect of RNA biochemistry including RNA editing, mRNA stability, localization and translation of transcripts, and in the activation of the RNA interference (RNAi) and microRNA (miRNA) pathways. Participation in these functions often requires restructuring the RNA molecules by the association of single-strand (ss) RNA-binding proteins or by the action of helicases. The Drosophila MLE helicase has long been identified as a member of the MSL complex responsible for dosage compensation. The complex includes one of two long non-coding RNAs and MLE was shown to remodel the roX RNA hairpin structures in order to initiate assembly of the complex. Here we report that this function of MLE may apply to the hairpins present in the primary RNA transcripts that generate the small molecules responsible for RNA interference. Using stocks from the Transgenic RNAi Project and the Vienna Drosophila Research Center, we show that MLE specifically targets hairpin RNAs at their site of transcription. The association of MLE at these sites is independent of sequence and chromosome location. We use two functional assays to test the biological relevance of this association and determine that MLE participates in the RNAi pathway.

Highlights

RNA hairpins are secondary structures formed by double-stranded regions, known as stems, with the paired strands connected by a terminal loop
During the fundamental processes of transcription and translation, these RNA structures are reshaped by helicases—enzymes that separate paired regions of nucleic acids
Small non-coding RNA molecules involved in regulating gene expression rely on sequences that allow them to form hairpin structures

Summary

Introduction

RNA hairpins are secondary structures formed by double-stranded (dsRNA) regions, known as stems, with the paired strands connected by a terminal loop. Hairpins can display a high level of heterogeneity in stem length, loop size, the number of bulges or internal loops present in the stem, and their thermodynamic properties [1]. Their function in the activation of the RNA interference (RNAi) and the microRNA (miRNA) pathways is well characterized [2]. Hairpin formation is required in a broad spectrum of gene-expression regulatory mechanisms, including RNA editing, mRNA stability, and the specific subcellular localization of transcripts and their translation [3,4]. The remodeling of RNA hairpins is achieved by association with singlestranded RNA (ssRNA) binding proteins, or by the action of helicases [11]

Methods

Results

Discussion

Conclusion