Nilges, B. S. | Search bioRxiv

bioRxiv2026

The small ORF (smORF)-encoded polypeptide MIRINE promotes neuronal differentiation in vertebrate brain development

The vertebrate brain expresses an extensive repertoire of long-noncoding RNAs (lncRNAs), an emerging source of small open reading frame (smORF)-encoded polypeptides (SEPs) whose functions remain largely unknown. Using ribosome profiling and proteomics of zebrafish and mouse brain, we identified hundreds of translated smORFs. We characterized MIRINE, a SEP of 83 amino acids conserved across 205 vertebrate species. MIRINE contains a transmembrane domain that targets it to the plasma membrane and intracellular vesicles, and is enriched in cortical and hippocampal neurons, with expression rising during neurogenesis. Downregulation of Mirine increased cell proliferation and impaired neuronal maturation in neuroblastoma cells, in mouse primary cortical neurons and cortex, and in the zebrafish forebrain, identifying MIRINE as a regulator of the balance between neuronal proliferation and differentiation. Mechanistically, MIRINE associates with the synaptic-vesicle protein Synaptogyrin-3 and related membrane proteins. Our findings define a conserved, membrane-associated SEP controlling neuronal maturation and illustrate the functional potential of brain SEPs.

biochemistry↗

bioRxiv2019

The translation inhibitor cycloheximide affects ribosome profiling data in a species-specific manner

Ribosome profiling provides genome-wide snapshots of translation dynamics by determining ribosomal positions at sub-codon resolution. To maintain this positional information, the translation inhibitor cycloheximide (CHX) has been widely used to arrest translating ribosomes prior to library preparation. Several studies have reported CHX-induced biases in yeast data casting uncertainty about its continued use and questioning the accuracy of many ribosome profiling studies. However, the presence of these biases has not been investigated comprehensively in organisms other than Saccharomyces cerevisiae. Here, we use a highly standardized and optimized protocol to compare different CHX-treatment conditions in yeast and human cells. Our data suggest that unlike in S. cerevisiae, translating ribosomes in human cells are not susceptible to conformational restrictions by CHX. Furthermore, CHX-induced codon-specific effects on ribosome occupancy are not detectable in human cells nor in other model organisms including Schizosaccharomyces pombe and Candida albicans. In fact, we find that even in S. cerevisiae most biases can be avoided by omitting CHX pre-treatment, indicating that other parameters of library generation contribute to differences between ribosome profiling experiments. Together our findings provide a framework for researchers who plan their own ribosome profiling experiments or who analyze published datasets to draw judicious conclusions.

molecular biology↗