Figure 1: Transcription and processing of mRNAs in trypanosomatids. The top part of the figure represents a hypothetical chromosome with three polycistronic gene clusters (PGC1-3). Pol II transcription initiates upstream of the first gene of the PGCs (arrows) [29, 38]. The G-run usually present at divergent strand-switch regions (SSR) is indicated. Nucleosomes located at the vicinity of transcription initiation regions contain histone variants H2AZ and H2BV [39]. The N-terminal tail of histone H3 in such nucleosomes are acetylated at K9/K14 (labeled as K9ac in the figure) and tri-methylated at K4 (K4me) [40, 41]. The N-terminal tail of histone H4 is acetylated at K10 (K10ac) [39], and at K5/K8/K12/K16 [41] (not shown in the figure). The bromodomain factor BDF3 [39], and transcription factors TRF4 and SNAP50 [40] also bind at transcription initiation regions. Pol II transcription of some PGCs terminates near tRNA genes (convergent strand-switch region between PGC2 and PGC3) [38], in regions of DNA that contain nucleosomes with histone variants H3V and H4V [39]. Transcription of a PGC produces a primary transcript (shown only for PGC2) that is processed by trans-splicing and polyadenylation to generate the mature mRNAs. By trans-splicing, a capped SL RNA (yellow box) is added to the 5 end of every mRNA. In the spliced leader locus (located in a different chromosome) each gene possesses a Pol II promoter region (arrows). The cap in the SL RNA is indicated by an asterisk at the 5 end of the RNA. The polycistronic transcript contains pyrimidine-rich regions (indicated by a striped box in the intergenic regions) that are needed for both trans-splicing and polyadenylation. The pyrimidine-rich regions are also present in the DNA, but they are not shown to simplify the figure. The four As located at the 3 end of the mature mRNAs represent the poly-A tail.