Fig. 1
Gene expression from DNA to mRNA in Trypanosoma brucei. The upper panel is a schematic time-lapse image of a polymerase II complex progressing along a chromosome. Coding regions are in dark colours and 3′ and 5′ untranslated regions are in lighter colours. The capped spliced leader is in orange. Kinetic constants for the different processes are indicated and the formulae that comprise the model are shown below the figure 5′ trans splicing (rate constant k1) and 3′ polyadenylation (rate constant k2) compete with nuclear degradation of the precursor (rate constant k3) and the 5′ spliced intermediate (rate constant k4). Assuming that the two processes are coupled, the rate constant for 3′ polyadenylation (k2) of mRNA A is expected to equal the rate constant for 5′ trans splicing (k1) of mRNA B, and the same applies for mRNA and mRNA C (k2 of mRNA B = k1 for mRNA C). Based on the observation that that long mRNAs had unexpectedly low abundances, we added a factor (α) that incorporates length-dependent precursor degradation into the model [16]. In the analysis described in this paper, we tested alternative versions of this and used a different factor for PC trypanosomes (see text and Table 1). Finally, there is degradation of the mature mRNA (rate constant k5). Values for k5 are based on transcriptome-wide decay measurements. In addition, the growth rate of the cells is included via the specific growth rate μ. The growth rate affects the abundance of every RNA species, as during growth the pre-existing RNA species get diluted