Genome-wide localization of histone variants in Toxoplasma gondii implicates variant exchange in stage-specific gene expression

Abstract

Background Toxoplasma gondii is a protozoan parasite that differentiates from acute tachyzoite stages to latent bradyzoite forms in response to environmental cues that modify the epigenome. We studied the distribution of the histone variants CenH3, H3.3, H2A.X, H2A.Z and H2B.Z, by genome-wide chromatin immunoprecipitation to understand the role of variant histones in developmental transitions of T. gondii parasites. Results H3.3 and H2A.X were detected in telomere and telomere associated sequences, whereas H3.3, H2A.X and CenH3 were enriched in centromeres. Histones H2A.Z and H2B.Z colocalize with the transcriptional activation mark H3K4me3 in promoter regions surrounding the nucleosome-free region upstream of the transcription start site. The H2B.Z/H2A.Z histone pair also localizes to the gene bodies of genes that are silent but poised for activation, including bradyzoite stage-specific genes. The majority of H2A.X and H2A.Z/H2B.Z loci do not overlap, consistent with variant histones demarcating specific functional regions of chromatin. The extent of enrichment of H2A.Z/H2B.Z (and H3.3 and H2A.X) within the entire gene (5’UTR and gene body) reflects the timing of gene expression during the cell cycle, suggesting that dynamic turnover of H2B.Z/H2A.Z occurs during the tachyzoite cell cycle. Thus, the distribution of the variant histone H2A.Z/H2B.Z dimer defines active and developmentally silenced regions of the T. gondii epigenome including genes that are poised for expression. Conclusions Histone variants mark functional regions of parasite genomes with the dynamic placement of the H2A.Z/H2B.Z dimer implicated as an evolutionarily conserved regulator of parasite and eukaryotic differentiation.

Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres

“…After defining the STs, we analyzed their chromatin architecture. Our detailed analysis of H2A.X, H3.3, and H3K9me3 enrichment throughout the subtelomeric region supports the heterochromatic composition of STs, as previously observed [ 31 ]. H3K9me3 is a recognized mark of repeat-rich constitutive heterochromatin [ 42 ].…”

“…Histone marks and variants were analyzed in every chromosome. The global histone analysis showed clear peaks for H3K9me3, H3.3, and H2A.X at regions delimiting the ends of the chromosomes [ 31 ]. A detailed analysis of ChIP-seq assays ( Table S2 ) showed that the intensities and/or peaks of these histones decreased from the chromosome end toward the centromere in most cases, being more evident for H3.3 and H2A.X ( Figure 2 A and Figure S1 ).…”

“…The histone H3K4me3 is a mark of transcription start sites (TSS)/promoters of active genes and colocalizes with histone variants H2A.Z and H2B.Z at almost all TSS/promoters of active genes [ 31 , 37 ]. Interestingly, it was suggested that the sole presence of H2A.Z/H2B.Z in a TSS is associated with the bivalent stage of chromatin.…”

“…Few cases of the sole presence of H2A.Z and/or H2B.Z in low-expression genes were observed. The presence of H3K4me3/H2A.Z/H2B.Z in the TSS region and 5′ end of active genes in T. gondii tachyzoites was recently observed, while the sole presence of H2A.Z/H2B.Z could be an indicator of a bivalent chromatin state [ 31 ]. In the T. gondii STs, a similar behavior for these histones was observed, suggesting that there is not a high level of bivalent genes.…”

“…In a separate set of ChIP-qPCR experiments, an enrichment of the heterochromatin marks H4K20me1 and H3K9me1 with the subtelomeric repetitive element sat350 was also detected [ 30 ]. Genome-wide analysis showed that H2A.X and H3.3 are also enriched at the chromosome ends [ 31 ].…”