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 . 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) , and at K5/K8/K12/K16  (not shown in the figure). The bromodomain factor BDF3 , and transcription factors TRF4 and SNAP50  also bind at transcription initiation regions. Pol II transcription of some PGCs terminates near tRNA genes (convergent strand-switch region between PGC2 and PGC3) , in regions of DNA that contain nucleosomes with histone variants H3V and H4V . 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 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 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 end of the mature mRNAs represent the poly-A tail.