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Open chromatin analysis in Trypanosoma cruzi life forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci

2022; BioMed Central; Volume: 15; Issue: 1 Linguagem: Inglês

10.1186/s13072-022-00450-x

1756-8935

Alex Ranieri Jerônimo Lima, Herbert Guimarães de Sousa Silva, Saloé Bispo Poubel, Juliana Nunes Rosón, Loyze Paola Oliveira de Lima, Héllida Marina Costa-Silva, Camila Silva Gonçalves, Pedro A. F. Galante, Fabíola Holetz, María Cristina M. Motta, Ariel Mariano Silber, Maria Carolina Elias, Júlia Pinheiro Chagas da Cunha,

Insect symbiosis and bacterial influences

Abstract Background Genomic organization and gene expression regulation in trypanosomes are remarkable because protein-coding genes are organized into codirectional gene clusters with unrelated functions. Moreover, there is no dedicated promoter for each gene, resulting in polycistronic gene transcription, with posttranscriptional control playing a major role. Nonetheless, these parasites harbor epigenetic modifications at critical regulatory genome features that dynamically change among parasite stages, which are not fully understood. Results Here, we investigated the impact of chromatin changes in a scenario commanded by posttranscriptional control exploring the parasite Trypanosoma cruzi and its differentiation program using FAIRE-seq approach supported by transmission electron microscopy. We identified differences in T. cruzi genome compartments, putative transcriptional start regions, and virulence factors. In addition, we also detected a developmental chromatin regulation at tRNA loci (tDNA), which could be linked to the intense chromatin remodeling and/or the translation regulatory mechanism required for parasite differentiation. We further integrated the open chromatin profile with public transcriptomic and MNase-seq datasets. Strikingly, a positive correlation was observed between active chromatin and steady-state transcription levels. Conclusion Taken together, our results indicate that chromatin changes reflect the unusual gene expression regulation of trypanosomes and the differences among parasite developmental stages, even in the context of a lack of canonical transcriptional control of protein-coding genes.