H3.3 demarcates GC-rich coding and subtelomeric regions and serves as potential memory mark for virulence gene expression in Plasmodium falciparum

Abstract

Histones, by packaging and organizing the DNA into chromatin, serve as essential building blocks for eukaryotic life. The basic structure of the chromatin is established by four canonical histones (H2A, H2B, H3 and H4), while histone variants are more commonly utilized to alter the properties of specific chromatin domains. H3.3, a variant of histone H3, was found to have diverse localization patterns and functions across species but has been rather poorly studied in protists. Here we present the first genome-wide analysis of H3.3 in the malaria-causing, apicomplexan parasite, P. falciparum, which revealed a complex occupancy profile consisting of conserved and parasite-specific features. In contrast to other histone variants, PfH3.3 primarily demarcates euchromatic coding and subtelomeric repetitive sequences. Stable occupancy of PfH3.3 in these regions is largely uncoupled from the transcriptional activity and appears to be primarily dependent on the GC-content of the underlying DNA. Importantly, PfH3.3 specifically marks the promoter region of an active and poised, but not inactive antigenic variation (var) gene, thereby potentially contributing to immune evasion. Collectively, our data suggest that PfH3.3, together with other histone variants, indexes the P. falciparum genome to functionally distinct domains and contribute to a key survival strategy of this deadly pathogen.

Apicomplexa and Histone Variants: What’s New?

“…CenH3, the centromere-specific H3, has been observed in animals, fungi, and plants [24] and also in Apicomplexa, including T. gondii, Plasmodium spp., and N. caninum [55]. This fact was recently confirmed by Fraschka et al [42] who found the centromeres depleted of PfH3.3 and PfH3, but occupied by PfCenH3. In T. gondii, this histone variant was characterized with the aim to understand the way in which chromosomes are delivered to the daughter cells after mitosis, a process that is still intriguing [21].…”

“…In Plasmodium, H3.3 had a similar expression pattern to another important histone variant, H2A.Z, namely localization to active chromatin [41] (see Figure 2). As observed in other eukaryotic cells, it has been recently demonstrated by ChiP-seq experiments that euchromatic regions in the genome are demarcated by the presence of the H3.3 variant histone [42].…”

“…Fraschka et al [42] have seen a particular correlation between enrichment in PfH3.3 histone variant and GC content, with this variant mainly located not only in euchromatic GC-rich sequences, but also in subtelomeric GC-rich repetitive regions. Interestingly, this correlation with the nucleotide composition is also observed with the double-variant nucleosome H2A.Z-H2B.Z (see below), but in this case, it is just the contrary: the regions with more AT content show abundance of this nucleosome [42]. However, GC-poor intergenic regions show the lowest H3.3 coverage, but the authors still argue that the incorporation of this variant to coding regions is more dependent on GC content than transcriptional activity.…”

“…However, in P. falciparum, there is a particular AT versus GC content along the genome with euchromatic intergenic regions richer in AT-content compared to coding sequences with less AT content [23]. Fraschka et al [42] have seen a particular correlation between enrichment in PfH3.3 histone variant and GC content, with this variant mainly located not only in euchromatic GC-rich sequences, but also in subtelomeric GC-rich repetitive regions. Interestingly, this correlation with the nucleotide composition is also observed with the double-variant nucleosome H2A.Z-H2B.Z (see below), but in this case, it is just the contrary: the regions with more AT content show abundance of this nucleosome [42].…”

“…Regarding this important gene family, H3.3 stably occupies the promoter region and coding sequence of the active var gene but is evidently less incorporated into the promoter and coding sequence of silenced var genes [42] (see Figure 3). Additionally, it has been demonstrated that the PTMs affecting histone H3 are extremely important in the regulation of var expression.…”