Molecular characterization of Snord116: ribosomal RNA interactions and impacts on neuronal protein translation

Abstract

Proper ribosome biogenesis and function are fundamental requirements for cellular protein synthesis and thus, organismal development. Ribosome biogenesis occurs in the nucleolus, where hundreds of proteins and RNAs interact with pre-ribosomal RNA (pre-rRNA) as it is transcribed and processed. Small nucleolar RNAs (snoRNAs) are essential regulators of ribosome biogenesis, typically guiding chemical modifications onto pre-rRNA via direct base-pair interactions. However, some snoRNAs lack assigned targets, limiting our understanding of their molecular functions. In particular, a subset of snoRNAs exhibit tissue-specific expression patterns, raising the possibility that snoRNAs could fine tune the ribosome to meet tissue-specific translational demands or serve other cell-type specific functions. Snord116 is a brain-enriched snoRNA with unknown molecular targets and functions. Loss of Snord116 is a critical driver of Prader-Willi Syndrome, a neurodevelopmental disorder characterized by dysregulated appetite and metabolic deficits. Snord116 exhibits many features of canonical snoRNAs, but prior studies have failed to identify ribosomal targets, leading to a prevailing hypothesis that Snord116 may have non-canonical functions independent of the ribosome. Defining the molecular targets and functions of Snord116 is critical to elucidate the molecular basis of Prader-Willi Syndrome and to understand how ribosome biogenesis factors may contribute to tissue-specific translational programs. Here, we comprehensively characterize Snord116 interactions in mouse neuronal systems using chimeric enhanced crosslinking and immunoprecipitation (chimeric eCLIP). We identify two direct interactions between Snord116 and 28S ribosomal RNA, and we validate these interactions in situ using proximity-dependent fluorescent imaging. Surprisingly, despite association with a core snoRNA-binding methyltransferase, we observe no methylation at Snord116 target sites. Instead, we find that Snord116 loss selectively impairs translation of specific neurodevelopmental genes during a critical developmental period in the mouse brain, without globally affecting protein translation. Together, this work identifies Snord116 as a neuron-enriched snoRNA that engages specific ribosomal targets through canonical mechanisms and for the first time, links Snord116 loss to impaired translation of genes critical for neurodevelopment.