The stress granule transcriptome reveals principles of mRNA accumulation in stress granules

By A. Khong, T. Matheny, Saumya Jain, Sarah F. Mitchell, Joshua R. Wheeler, R. Parker. Molecules and Cells, 2017

696 citations recorded by the source corpus.

SUMMARY Stress granules are mRNA-protein assemblies formed from nontranslating mRNAs. Stress granules are important in the stress response and may contribute to some degenerative diseases. Here we describe the stress granule transcriptome of yeast and mammalian cells through RNA-Seq analysis of purified stress granule cores and smFISH validation. While essentially every mRNA, and some ncRNAs, can be targeted to stress granules, the targeting efficiency varies from <1% to >95%. mRNA accumulation in stress granules correlates with longer coding and UTR regions and poor translatability. Quantifying the RNA-Seq analysis by smFISH reveals only 10% of bulk mRNA molecules accumulate in mammalian stress granules, and only 185 genes have more than 50% of their mRNA molecules in stress granules. These results suggest stress granules may not represent a specific biological program of mRNP assembly, but instead form by condensation of nontranslating mRNPs in proportion to their length and lack of association with ribosomes.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ecf228513512bcf4ebf1e30ecb2597b99f2bb6cb

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LNCcation: lncRNA localization and function (2021, methodology): “, 2019) tracking the dynamics of individual lncRNAs with PB foci suggests that the transient nature of interactions of lncRNAswith the periphery of PBs may make it difficult to capture lncRNA PB/SG interactors with the biochemical isolation methods used by previous transcriptome inventories (Khong e”
G3BP1 is a tunable switch that triggers phase separation to assemble stress granules (2020, positive): “The hits from the confirmatory screen (SSMD ≤ −1.5) were further tested in a deconvolution screen where we tested the individual siRNAs for the targeted gene in quadruplicate.”