Replication origin location might contribute to genetic variability in Trypanosoma cruzi

Abstract

Background: DNA replication in trypanosomatids operates in a uniquely challenging environment, since most of their genomes are constitutively transcribed. Trypanosoma cruzi, the etiological agent of Chagas disease, presents high variability in both chromosomes size and copy number among strains, though the underlying mechanisms are unknown. Results: Here we have mapped sites of DNA replication initiation across the T. cruzi genome using Marker Frequency Analysis, which has previously only been deployed in two related trypanosomatids. The putative origins identified in T. cruzi show a notable enrichment of GC content, a preferential position at subtelomeric regions, coinciding with genes transcribed towards the telomeres, and a pronounced enrichment within coding DNA sequences, most notably in genes from the Dispersed Gene Family 1 (DGF-1). Conclusions: These findings suggest a scenario where collisions between DNA replication and transcription are frequent, leading to increased genetic variability, as seen by the increase SNP levels at chromosome subtelomeres and in DGF-1 genes containing putative origins.

Nucleosome landscape reflects phenotypic differences in Trypanosoma cruzi life forms

“…From the selected dynamic nucleosomes with FDRs lower than 0.01 (totaling 3499 IDs, or 33% of the total IDs), we verified that 80% of DGF-1 genes have at least one dynamic nucleosome (Fig 6A), which is in clear contrast with other gene classes. Interestingly, this is not due to a larger total length (in bp) of DGF-1 genes, as TS genes occupy as much of the genome as DGF-1 genes (S11A Fig) . In addition, when normalized by total length in kbp, DGF-1 genes had more dynamic nucleosomes per kbp than all other gene classes (S11A Fig) . Recently, we detected that replicative origins are preferentially located at DGF-1 genes, and we proposed that genetic variability may be induced due to frequent collisions between replication and transcription machineries [50]. Here, we detected that this gene class is also more likely to have dynamic nucleosomes (S11B Fig).…”

Genomic Organization and Generation of Genetic Variability in the RHS (Retrotransposon Hot Spot) Protein Multigene Family in Trypanosoma cruzi

“…Gene conversion has been proposed as an active force in the evolution of trypanosomes [ 65 ]. Araujo et al, 2020 [ 66 ] showed that DNA replication origins in T. cruzi are preferentially located at the subtelomeric region, which is a site of conflict between transcription and replication that may lead to DNA double-strand breaks and generation of diversity. Wier et al, 2016 [ 67 ] suggested that gene conversion is the mechanism used by T. brucei gambiensis to avoid the Meselson effect of accumulation of mutations on the chromosomes for lack of sexual recombination in this species.…”

Trypanosoma Cruzi Genome: Organization, Multi-Gene Families, Transcription, and Biological Implications

“…Regarding T. cruzi , the ORIs of CL Brener strain were recently analyzed by MFA-seq [ 86 ], mapping 103 and 110 putative consensus ORIs in each haplotype of this hybrid strain. Moreover, the analysis displayed that some replication initiation sites map to the borders of the transcription units, as in Leishmania major and T. brucei .…”

“…Considering the chromosomal location, while some ORIs of T. cruzi are located in non-transcribed regions as those seen in T. brucei and Leishmania major , many others are strategically localized at sub-telomeric regions (with a strong focus on DGF-1 genes), where they can produce genetic variability of multi-gene families [ 86 ]. The transcription orientation toward telomeres suggests that the abundance of putative ORIs in sub-telomeric regions produces head-on transcription-replication collisions since the replisomes go toward the centers of the chromosomes.…”

“…The transcription orientation toward telomeres suggests that the abundance of putative ORIs in sub-telomeric regions produces head-on transcription-replication collisions since the replisomes go toward the centers of the chromosomes. These results suggest that collisions between DNA replication and transcription are recurrent in the T. cruzi genome and produce genetic variability, as suggested by the increase in SNP levels in the sub-telomeric regions and the DGF-1 genes containing putative ORIs [ 86 ].…”