Fig. 1: Determining the kinetics of post-transcriptional events.
From: Kinetics of mRNA nuclear export regulate innate immune response gene expression
A Following mRNA from transcription to degradation. First, the mRNA is attached to the chromatin (caRNA), then it is released to the nucleoplasm (npRNA) upon 3′-cleavage, finally it is transported to the cytoplasm where it is degraded. B Schematic of the experimental setup. Bone-marrow-derived macrophages (BMDMs) are stimulated with LPA. Cells are harvested at different time after stimulation and fractionated into subcellular fractions, and RNA is extracted. C Example of tracks for the Tnf gene. Many intronic reads are found in the chromatin-associated fraction, fewer in the nucleoplasmic fraction, and the cytoplasmic fraction RNA is fully spliced. D Gene selection workflow. Lowly expressed genes were filtered out, and inducible genes at the chromatin level were selected. E Heatmap of gene expression of the selected genes in (D) for each fraction. F Correlation analysis of mRNA abundance in each fraction. Note a stronger correlation between chromatin and nucleoplasmic fraction for nearby timepoints than between nucleoplasmic and cytoplasmic fractions or between cytoplasmic and chromatin fractions. Also, note a time shift, that timepoints on the chromatin correlate better with later timepoints in the cytoplasmic fraction. G Example genes: Top, Cd74 and Btg2 have similar chromatin expression profiles but exhibit different profiles in the nucleoplasmic and cytoplasmic fraction. Bottom, Arl5b and Ccr3 show similar cytoplasmic levels but Arl5b expression is few fold higher than Ccr3 in both chromatin and nucleoplasmic fractions.
