Journal Article

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

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

2022

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Active chromatin / Analysis / Animal Genetics and Genomics / Biomedical and Life Sciences / Cell Biology / Cell differentiation / Chromatin / Chromatin - genetics / Chromatin - metabolism / Chromatin Assembly and Disassembly / Chromatin remodeling / Developmental stages / Epigenetic inheritance / Epigenetics / FAIRE-seq / Gene clusters / Gene Expression / Gene expression control / Gene Expression Regulation / Gene Function / Gene regulation / Genes / Genetic aspects / Genetic research / Genetic transcription / Genomes / Genomics / Human Genetics / Life Sciences / Morphology / Parasites / Plant Genetics and Genomics / Polycistronic transcription / Post-transcription / Proteins / Proteomics - methods / Transcriptomics / Transfer RNA / Transmission electron microscopy / tRNA / Trypanosoma cruzi / Trypanosoma cruzi - genetics / Trypanosoma cruzi - metabolism / Virulence / Virulence factors