Intrinsic DNA curvature in trypanosomes

Abstract

Background: Trypanosoma cruzi and Trypanosoma brucei are protozoan parasites causing Chagas disease and African sleeping sickness, displaying unique features of cellular and molecular biology. Remarkably, no canonical signals for RNA polymerase II promoters, which drive protein coding genes transcription, have been identified so far. The secondary structure of DNA has long been recognized as a signal in biological processes and more recently, its involvement in transcription initiation in Leishmania was proposed. In order to study whether this feature is conserved in trypanosomatids, we undertook a genome wide search for intrinsic DNA curvature in T. cruzi and T. brucei.

Results: Using a region integrated intrinsic curvature (RIIC) scoring that we previously developed, a non-random distribution of sequence-dependent curvature was observed. High RIIC scores were found to be significantly correlated with transcription start sites in T. cruzi, which have been mapped in divergent switch regions, whereas in T. brucei, the high RIIC scores correlated with sites that have been involved not only in RNA polymerase II initiation but also in termination. In addition, we observed regions with high RIIC score presenting in-phase tracts of Adenines, in the subtelomeric regions of the T. brucei chromosomes that harbor the variable surface glycoproteins genes.

Conclusions: In both T. cruzi and T. brucei genomes, a link between DNA conformational signals and gene expression was found. High sequence dependent curvature is associated with transcriptional regulation regions. High intrinsic curvature also occurs at the T. brucei chromosome subtelomeric regions where the recombination processes involved in the evasion of the immune host system take place. These findings underscore the relevance of indirect DNA readout in these ancient eukaryotes.

Keywords: Base J; DNA intrinsic curvature; Transcription; Trypanosoma; VSG; brucei; cruzi.

Fig. 1

Graphical representation of sequence dependent curvature. A schematic representation of the indicated trypanosomatid chromosomes are presented. Upper panel: Bar plots of chromosome positions with an IC value greater than 13  per helical turn. Middle panel: bar plots of chromosome positions with an RIIC value greater than the selected cutoff. Lower panel: both DNA strands are depicted in grey, overlaid with CDS features shown in blue. Features labeled as ncRNA, snRNA or snoRNAs are shown in green. tRNAs are shown in red. Assembly gaps are shown in brown. For T. brucei chromosome 5 subtelomeric VSG clusters are underlined

Fig. 2

Overlap analysis of high RIIC in T. cruzi SSRs. Strand switch regions were identified and their RIIC scores calculated. The bar plot shows the number of DSSR and CSSR regions overlapping high RIIC scoring regions (dark grey) and non-overlapping (light grey)

Fig. 3

Graphical representation of transcription markers’ signals and sequence dependent curvature RIIC score in T. brucei. For T. brucei chromosome 4, the graphical representation of regions with RIIC value greater than the selected cutoff (lower panel) are shown above the schematic representation of both chromosome DNA strands depicted in grey, overlaid with CDS features shown in blue. Modified histone locations (H4K10ac) from [17] and base J from [12] are indicated as following: regions associated to H4K10ac but not associated with base J (*); regions associated to H4K10ac and also with base J (!); regions associated with base J and not with H4K10ac (+). Features labeled as ncRNA, snRNA or snoRNAs are shown in green. tRNAs are shown in red. Assembly gaps are shown in brown

Fig. 4

Logo representation of the main motif found by MEME analysis around high curvature peaks in T. brucei subtelomeric VSG clusters. The sequences surrounding high IC peaks were analyzed by MEME as described in Materials and “Methods”, and the logo representation for the most significant motif is shown