Journal: Molecular cell
Article Title: Transcriptome-wide mRNP condensation precedes stress granule formation and excludes new mRNAs
doi: 10.1016/j.molcel.2025.11.003
Figure Lengend Snippet: (A) Analysis of mRNA condensation by sedimentation and RNA sequencing (Sed-seq) enables calculation of mRNA proportion in the supernatant (pSup) across conditions. (B) 15 min of heat shock induces SG formation at 46°C but not at 42°C, as marked by poly(A)-binding protein (Pab1-HaloTag) and FISH against poly(A)+ RNA (scale bar, 5 μm). (C) Comparison of protein condensation (data from Wallace et al.) and mRNA condensation (this study), and points show individual genes (protein or mRNA) (violin plot; median). (D) Transcript pSup decreases with length under all conditions, including in unstressed cells at 30°C. Stress induces additional shifts in sedimentation beyond this baseline. Each point represents a single gene’s transcripts at a given temperature, with the solid black line showing the mean pSup for transcripts of that length. PMU1 mRNA, highlighted with a black border, sediments like a transcript more than three times its expected size following 42°C heat stress (dotted line). (E) A simple clustering model (see ) captures average pSup and stress-induced changes. Vertical boundaries mark the 1st and 99th percentiles of transcripts by length. (F) Sed-seq data allow quantification of key features: differential sedimentation relative to control (ΔSed) and escape from sedimentation (eSed). Both ΔSed and eSed control for effects of transcript length and are in units of σ, the standard deviation (SD) in sedimentation (dotted lines) around the length-dependent mean (solid lines); see . (G) Top: virtually all transcripts (gray points/density) sediment in response to 42°C heat shock, i.e., condensation, indicated by ΔSed > 0. Bottom: most genes (83%) in the heat shock factor 1 (Hsf1) regulon (orange points/density) show significant escape from sedimentation (eSed > 0). See also .
Article Snippet: Custom Stellaris ® RNA FISH Probes were designed against SSB1, SSA4, HSP104, and ADD66 by utilizing the Stellaris ® RNA FISH Probe Designer (Biosearch Technologies, Inc., Petaluma, CA) available online at www.biosearchtech.com/stellarisdesigner ( ).
Techniques: Sedimentation, RNA Sequencing, Binding Assay, Comparison, Control, Standard Deviation
