The nucleosome landscape ofPlasmodium falciparumreveals chromatin architecture and dynamics of regulatory sequences

Abstract

In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-associated processes and it is central to the control of gene expression. For Plasmodium falciparum, a causative agent of human malaria, the nucleosome positioning profile of regulatory regions deserves particular attention because of their extreme AT-content. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit by demarcating landmark sites (transcription/translation start and end sites). In addition, our analysis provides strong indications for the function of positioned nucleosomes in splice site recognition. Transcription start sites (TSSs) are bordered by a small nucleosome-depleted region, but lack the stereotypic downstream nucleosome arrays, highlighting a key difference in chromatin organization compared to model organisms. Furthermore, we observe transcription-coupled eviction of nucleosomes on strong TSSs during intraerythrocytic development and demonstrate that nucleosome positioning and dynamics can be predictive for the functionality of regulatory DNA elements. Collectively, the strong nucleosome positioning over splice sites and surrounding putative transcription factor binding sites highlights the regulatory capacity of the nucleosome landscape in this deadly human pathogen.

Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

“…However, these results are based on highly over-digested chromatin and it is known that MNase exhibits a strong preference for AT-rich sequences [40]. A recent genome wide study shows that nucleosomes in the intergenic regions are not depleted, but potentially disappear by over-digestion of chromatin with MNase [16]. Analyzing the new, low digested dataset, still revealed higher nucleosome occupancy at GC-rich sequences (S4D and S4E Fig).…”

“…Next, we had a closer look at the available high throughput sequencing data and re-analyzed the datasets studying the accessibility of chromatin (Data sets used: SRX013309 [14], SRX013302 [14], SRX885811-SRX885819 [16]). Ponts and colleagues performed FAIRE assays [39] to reveal the accessible genomic regions, relative to their MNase resistant nucleosomal fraction.…”

“…Also for plasmodium it was shown that proper promoter functioning and regulation of var gene expression requires the presence of positioned nucleosomes [10–13]. High-throughput sequencing analyses of nucleosome positions and chromatin structure analyses in different life cycle stages correlate changes in chromatin structure with the regulation of gene expression [14–16]. Interestingly, the chromatin structure of P .…”

Comparative Bioinformatics Analysis of Transcription Factor Genes Indicates Conservation of Key Regulatory Domains among Babesia bovis, Babesia microti, and Theileria equi

“…Regulation of gene expression in eukaryotic cells can be achieved at the transcriptional level using both genetic and epigenetic mechanisms. Moreover, it is likely that the activity of transcription factors and DNA binding proteins, combined and acting in coordination with modulated chromatin organizations such as nucleosome positioning, essentially controls gene expression at different parasite life cycle stages [7]. In addition, gene expression can also be regulated at the post-transcriptional and translational levels.…”

“…equi AP2 domains remain unknown, and they will need to be defined experimentally. Remarkably, the specificity of binding of some AP2 proteins to certain short DNA target motifs (usually six to seven base-pairs long) appears to be quite conserved among distinct Plasmodium species and, furthermore, among other related apicomplexans [7, 25]. These findings suggest that Plasmodium binding specificity data together with bioinformatics analysis on the 5′ upstream gene coding regions could guide the design of future experiments aimed at establishing the DNA binding specificities of the AP2 proteins in the three parasites examined in this study.…”