Extended Data Fig. 9: Distinct nascent RNA kinetics in zebrafish and HeLa nucleoli.
From: Pre-rRNA spatial distribution and functional organization of the nucleolus
a. Spatial organization of pre-rRNA segments in ZF4 cells and zebrafish embryos. Left, diagram of zebrafish pre-rRNA processing pathway with smFISH probe positions (magenta lines). Right, representative images showing localization of various pre-rRNA segments in ZF4 cells. Zebrafish Fbl (Z-Fbl, green) labels the FZ compartment. Probes targeting early processing intermediates (5′ ETS, ITS1, ITS2) show signal enrichment within or adjacent to the FZ, while probes targeting mature sequences (18S and 28S) primarily label transcripts in the outer granular zone (GZ), indicating a spatial separation of early and late processing steps. b. Representative averaged images of nascent pre-rRNAs (magenta) and Fbl (green) at the sequential labelling time points in zebrafish embryos. Fbl marks the FZ. See also Fig. 4d. c. Representative averaged images of nascent pre-rRNAs (magenta) and FBL (green) at sequential labelling time points in HeLa nucleoli. FBL marks the DFC. See also Fig. 4e. d. Representative whole-nucleus images of nascent pre-rRNAs and Fbl in zebrafish embryos with quantification of nascent rRNA intensities at different time points (right), n = 13, 12, 22, 15, 11cells over time points. e. Representative whole-nucleus images of nascent pre-rRNAs and FBL in HeLa cells with quantification of nascent rRNA intensities at different time points (right), n = 15 cells per time point. d, e Curves are fitted using one-phase association. The stable intensity of Pol II-transcribed nascent RNAs (nucleoplasm distributed) over the continuous labelling period excludes the possibility that 5-EU exhaustion can cause the reduced nascent pre-rRNA signals within the innermost FC region.
