RGS4 RNA Secondary Structure Mediates Staufen2 RNP Assembly in Neurons

Abstract

RNA-binding proteins (RBPs) act as posttranscriptional regulators controlling the fate of target mRNAs. Unraveling how RNAs are recognized by RBPs and in turn are assembled into neuronal RNA granules is therefore key to understanding the underlying mechanism. While RNA sequence elements have been extensively characterized, the functional impact of RNA secondary structures is only recently being explored. Here, we show that Staufen2 binds complex, long-ranged RNA hairpins in the 3′-untranslated region (UTR) of its targets. These structures are involved in the assembly of Staufen2 into RNA granules. Furthermore, we provide direct evidence that a defined Rgs4 RNA duplex regulates Staufen2-dependent RNA localization to distal dendrites. Importantly, disrupting the RNA hairpin impairs the observed effects. Finally, we show that these secondary structures differently affect protein expression in neurons. In conclusion, our data reveal the importance of RNA secondary structure in regulating RNA granule assembly, localization and eventually translation. It is therefore tempting to speculate that secondary structures represent an important code for cells to control the intracellular fate of their mRNAs.

RNA supply drives physiological granule assembly in neurons

“…To test whether RBPs involved in RNA transport would supply RNAs needed for DDX6 granule formation, we focused on the double-stranded RBP Stau2, which we have previously identified as an interaction partner of DDX6 in neurons 18 . Stau2 recognizes complex RNA secondary structures predominantly in the 3' untranslated region (UTR) of its targets and is an essential RNA transport protein responsible for localizing a significant fraction of the neuronal transcriptome within different cellular compartments 30,[33][34][35][36] . A DEAD box RNA helicase such as DDX6 may play a role in the regulation of such complex targets.…”

“…In addition to RNA availability, we have recently identified RNA secondary structures as another important feature in the process of RNA granule assembly. Here, specific RNA hairpins bound by Stau2 regulate granule assembly, translatability, and dendritic transport of target RNAs 36 . Consequently, RNAs can drive granule assembly not only through sequences but also through secondary structures in vivo.…”

A positive feedback circuit between RN7SK snRNA and m6A readers is essential for tumorigenesis

“…The secondary structure of RNA is important and closely linked to functions for mRNAs and non-coding RNAs, including snRNAs. 49 , 50 When bound by RBPs, RNA secondary structures form higher-order tertiary structures and confer catalytic, regulatory and scaffolding functions. 51 RNA secondary structure is also essential for RN7SK to absorb exonucleases and interfere with their functions to degrade m 6 A reader mRNA.…”

RNA-Binding Proteins as Epigenetic Regulators of Brain Functions and Their Involvement in Neurodegeneration

“…From this point of view, a particularly interesting protein with prion-like domains seems to be the already mentioned CPEB protein, indeed required for LTM [ 147 ]. One interesting possibility is that the secondary structure of the included RNAs is what would also (or even primarily) regulate the stabilization of the RBP structure, thus allowing protein binding and assembly of the granules, which are then involved in RNA transport, localization, and translation [ 157 ].…”