Fig. 3: Features driving RNA localization.

a, Cytosol (Cyt), nucleus (Nuc) and membrane (Mem) proportions for mRNAs and lncRNAs. b, Empirical cumulative frequency distributions for nucleus proportions for mRNAs and lncRNAs. c, Coefficient estimates for logistic regression model of lncRNA cytosol proportions. P values derived from two-tailed z-test. d, Proportions for mRNAs encoding signal peptides and/or TM domains. e, Membrane proportions for mRNAs shown in d. f, GO terms significantly enriched in mRNAs not encoding signal peptides and/or TM domains but over 35% membrane localized. P values derived from a two-tailed hypergeometric test and adjusted for multiple testing using the Benjamini–Hochberg FDR correction. CC, cell compartment. MF, molecular function. g, smFISH/IF images of digitonin-extracted (Dig+) and control (Dig−) U-2 OS cells co-stained for the ER (calnexin, magenta), and MACF1 and DST RNAs (green). Calpain2 and PIGT RNAs are shown as examples of cytosolic transcripts and known ER transcripts, respectively. Scale bar, 10 μm. h, Quantification of RNA transcripts in digitonin-treated cells, using control (untreated) cells for normalization. At least 30 cells were quantified per condition. ****P < 0.0001 (two-tailed Mann–Whitney U test).