Trypanosoma cruzi nascent transcriptome identified similar transcription levels among canonical PTUs and identified critical differences between conserved and virulence genomic compartments.

Trypanosomatids are organisms that diverged early in the eukaryotic lineage and have some unusual features such as polycistronic transcription and trans-splicing. In these organisms, post-transcriptional mechanisms are identified as the main responsible for gene expression regulation, although current and past findings suggest that additional layers of regulation may also play a role. Here, we performed a genome-wide nascent transcriptomic analysis from Trypanosoma cruzi to understand the real impact of transcription on gene expression regulation. We detected an asymmetrical distribution of transcription abundance along all genomic features and that approximately 9% of genome has undetectable transcription levels. Focusing on protein-coding genes transcripts, we observed that genomic regions associated with conserved and trypanosamatids syntenic genes (the core genomic compartment) are more transcribed than those associated with virulence and non-syntenic (the disruptive genomic compartment). Moreover, PTUs enriched in core genes have differential expression related to the number of CDSs, which is not observed for disruptive PTUs. In general, PTUs from core compartment that have similar amount of CDSs per PTU have similar transcription expression. Among them, only 10% of PTUs have differential nascent expression. Strickling, virulence genes located into a core-enriched PTU are more abundant than those located in a disruptive-enriched PTUs, and are overrepresented in ineffective forms, suggesting a transcription regulation mechanism based on genome organization that may have a strong importance for selecting critical virulence genes to be expressed. The presence of regions coding for non-coding small RNAs (such as tRNAs and snoRNAs) in vicinities of PTUs also affect gene expression, pointing out to another role of genomic organization for gene expression. Finally, we found that genomic regions that are more transcribed have a higher level of open chromatin, as well as PTUs associated to open regions at transcription start sites. In sum, our results pointing out not all genomic regions are equally transcribed wth critical differences in genomic compartments, although canonical core PTUs with similar number of CDSs have a similar expression. Together, T. cruzi gene expression may be also regulated by the epigenetic landscape and genomic organization beyond the well-known posttranscriptional mechanisms.