A′-form RNA helices are required for cytoplasmic mRNA transport in Drosophila

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Abstract
The Drosophila fs(1)K10 transcript is localized asymmetrically during oogenesis through a cis-acting RNA element called the TLS. The tertiary structure of this hairpin is now presented, and while it contains W-C base pairs, the RNA helix takes on an A' form conformation that is needed for correct subcellular targeting. Microtubule-based mRNA transport is widely used to restrict protein expression to specific regions in the cell and has important roles in defining cell polarity and axis determination as well as in neuronal function. However, the structural basis of recognition of cis-acting mRNA localization signals by motor complexes is poorly understood. We have used NMR spectroscopy to describe the first tertiary structure to our knowledge of an RNA element responsible for mRNA transport. The Drosophila melanogaster fs(1)K10 signal, which mediates transport by the dynein motor, forms a stem loop with two double-stranded RNA helices adopting an unusual A′-form conformation with widened major grooves reminiscent of those in B-form DNA. Structure determination of four mutant RNAs and extensive functional assays in Drosophila embryos indicate that the two spatially registered A′-form helices represent critical recognition sites for the transport machinery. Our study provides insights into the basis for RNA cargo recognition and reveals a key biological function encoded by A′-form RNA conformation.