Nucleosome landscape reflects phenotypic differences in Trypanosoma cruzi life forms

Abstract

Trypanosoma cruzi alternates between replicative and nonreplicative life forms, accompanied by a shift in global transcription levels and by changes in the nuclear architecture, the chromatin proteome and histone posttranslational modifications. To gain further insights into the epigenetic regulation that accompanies life form changes, we performed genome-wide high-resolution nucleosome mapping using two T. cruzi life forms (epimastigotes and cellular trypomastigotes). By combining a powerful pipeline that allowed us to faithfully compare nucleosome positioning and occupancy, more than 125 thousand nucleosomes were mapped, and approximately 20% of them differed between replicative and nonreplicative forms. The nonreplicative forms have less dynamic nucleosomes, possibly reflecting their lower global transcription levels and DNA replication arrest. However, dynamic nucleosomes are enriched at nonreplicative regulatory transcription initiation regions and at multigenic family members, which are associated with infective-stage and virulence factors. Strikingly, dynamic nucleosome regions are associated with GO terms related to nuclear division, translation, gene regulation and metabolism and, notably, associated with transcripts with different expression levels among life forms. Finally, the nucleosome landscape reflects the steady-state transcription expression: more abundant genes have a more deeply nucleosome-depleted region at putative 5’ splice sites, likely associated with trans-splicing efficiency. Taken together, our results indicate that chromatin architecture, defined primarily by nucleosome positioning and occupancy, reflects the phenotypic differences found among T. cruzi life forms despite the lack of a canonical transcriptional control context.

Histone H2B.V demarcates strategic regions in the Trypanosoma cruzi genome, associates with a bromodomain factor and affects parasite differentiation and host cell invasion

“…It is well known that global transcription levels are decreased in TCTs in relation to epimastigote forms [25], and similar findings have been found in T. brucei [53,54]. Recently, we observed that dSSRs in TCTs have more nucleosomes, which are less dynamic than those from epimastigote forms [27]. Here, we detect that H2B.V is predominantly located at dSSRs of epimastigotes but very few H2B.V enrichment peaks were found on TCTs’ genome.…”

“…We hypothesized that either H2B.V was spread along the TCT genome or weakly bound to TCT chromatin in comparison to epimastigotes. Nucleosomes harboring H2B.V-H2A.Z are less stable than canonical nucleosomes [12], and their absence could (partially) explain why dSSRs of TCTs were more occupied by nucleosomes than epimastigotes [27]. We speculate that the absence of histone variants would result in a more stable chromatin structure around dSSRs that, in turn, could hamper RNA Pol II binding, likely explaining the decreased global levels of transcription in this life form [25].…”

“…(A) Total reads and overall alignment of input and H2B.V-ChIP samples in the CL Brenerr Esmeraldo-like haplotype (release 32) and TCC (release 44) assemblies. (B) H2B.V peaks identified in epimastigotes and TCTs using a peak calling algorithm available in HOMER [27] considering a fold enrichment of 4 (default) (green bars) and 2 (orange bars) and a required Poisson p-value over input = 1.00e-04. Left, number of peaks obtained at each replicate (R) separately.…”

“…Changes in nuclear and chromatin structure together with a global change in transcription rate follow the differentiation of replicative and noninfective forms (epimastigote and amastigote) to nonreplicative and infective forms (tissue culture-derived trypomastigote and metacyclic trypomastigote (TCT and MT, respectively) [25,26]. Furthermore, the nucleosome landscape of epimastigotes and TCTs differs mainly at dSSRs [27]. In addition to these alterations, parasite histones are differentially modified by methylation, acetylation and phosphorylation during the cell cycle and differentiation [28–34].…”

Experimental and Bioinformatic upgrade for genome-wide mapping of nucleosomes in Trypanosoma cruzi

“…This phenomenon is suspected to be due to the unique characteristic of its histone H1, which lacks the globular domains typically present in other eukaryotes (Toro and Galanti, 1988). Besides, the infective and non-infective parasite life forms display different levels of chromatin condensation during interphase (Hecker and Gander, 1985), differential susceptibility to DNaseI (Spadiliero et al, 2002) and some differences in the nucleosome landscape (Lima et al, 2021). Additionally, the histones of trypanosomes are the least conserved among all eukaryotic histones studied so far, differing from other organisms in size, sequence, and charge (Toro and Galanti, 1988; Thatcher and Gorovsky, 1994).…”