RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome

Ribonucleoprotein (RNP) granules are non-membrane bound organelles thought to assemble by protein-protein interactions of RNA-binding proteins. We present evidence that a wide variety of RNAs self-assemble in vitro into either liquid-liquid phase separations or more stable assembles, referred to as RNA tangles. Self-assembly in vitro is affected by RNA length, ionic conditions, and sequence. Remarkably, self-assembly of yeast RNA in vitro under physiological salt mimics the composition of mRNAs within yeast stress granules. This suggests that the biophysical principles that drive RNA self-assembly in vitro contribute to determining the stress granule transcriptome. Consistent with RNA self-assembly contributing to RNP granule formation, an excess of purified RNA injected into C. elegans syncytium coalesces into droplet-like assemblies. We suggest that diverse RNA-RNA interactions in trans contribute to RNP granule formation and may explain the prevalence of large RNA-protein assemblies in eukaryotic cells. Overall design: RNA mixtures were assembled at 150mM NaCl, 10%PEG, 1mM MgCl2 and 150ug/mL total yeast RNA for comparison against total yeast RNA. RNA assemblies were pelleted and sent to the University of Colorado BioFrontiers Institute Next-Gen Sequencing Core Facility for Ribo-Zero treatment, library construction and NextSeq run.

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Van Treeck B, Protter DSW, Matheny T, Khong A, Link CD, Parker R