Epigenetics, a field with many unresolved questions, is particularly interested in the role of chromatin structure modulation and its epigenetic marks in relation to transcriptional regulation. Our investigation will utilize a simple eukaryotic cell model, Trypanosoma cruzi, to delve into this question. These organisms, which hold significant medical relevance in Latin America, lack gene-specific transcriptional regulation for most transcripts. This allows us to observe the effects of epigenome dynamics without the interference of transcriptional regulation. Epigenetic marks and global changes in chromatin structure have been documented in trypanosomes, and there’s evidence suggesting their modulation during cell differentiation. We plan to study the epigenome throughout cell differentiation from epimastigote to metacyclic trypomastigote forms using techniques like Gro-seq, Faire-seq, and quantitative proteomics. By integrating the results, we aim to shed light on crucial questions in the field of epigenetics.