Extended Data Fig. 4: Capture of GA-multivalent mRNAs within nuclear speckles driven by R-MCD concentration.
From: Collective homeostasis of condensation-prone proteins via their mRNAs
a, Normalised counts for the nuclear lncRNA NEAT1 and the efficiently exported mRNA RPL12 in nuclear and cytoplasmic fractions at different PPIGLCD expression timepoints. b, Normalised counts for control (PSAP, HNRNPDL) and GA-rich (EIF3A, BRD4) RNAs, as in panel a. c, Co-localisation of mScarlet-PPIGLCD with nuclear speckles. d, Oligo-dT FISH of cells expressing mScarlet-PPIGLCD. e, Changes in the nuclear SC35 intensity and the size and number of speckles per nucleus after expression of mScarlet-PPIGLCD across 3 replicates, with at least 100 nuclei per replicate. f, The ratio of total oligo-dT FISH signal in the nucleus and cytoplasm per cell compared the the intensity of mScarlet-PPIGLCD in the nucleus. Points are coloured based on the length of expression induction with doxycycline. g, The ratio of the upper quartile to the median of nuclear oligo-dT FISH signal as a proxy for the relative intensity of nuclear speckle signal. Ratios are compared the intensity of mScarlet-PPIGLCD in the nucleus, and points are coloured as in panel f. h-i, Example images showing HCR-FISH signal for HNRNPDL (control) or BRD4 (GA-multivalent) mRNAs, with SC35 immunofluorescence and mScarlet-PPIGLCD. j, Quantification of the enrichment of HCR-FSH signal within nuclear speckles versus nucleoplasm per nucleus with respect to PPIGLCD expression. 3 independent replicates are plotted in different colours and regression lines are plotted in dashed lines. k, The fits of linear regression models (R2) of the relationship between mScarlet-PPIGLCD expression and mRNA enrichment within the speckle for control and GA-multivalent mRNAs for each of the 3 replicates. l, Quantification of the proportion of total R-MCD encoding transcripts or total mRNAs that are the overexpressed PPIGLCD transcript in the dox induction time course sequencing experiment. m, Quantification of the abundance of all R-MCD proteins or the overexpressed mScarlet-PPIGLCD after 12 h of doxycycline induction.
