Expression of P. falciparum var Genes Involves Exchange of the Histone Variant H2A.Z at the Promoter

Abstract

Plasmodium falciparum employs antigenic variation to evade the human immune response by switching the expression of different variant surface antigens encoded by the var gene family. Epigenetic mechanisms including histone modifications and sub-nuclear compartmentalization contribute to transcriptional regulation in the malaria parasite, in particular to control antigenic variation. Another mechanism of epigenetic control is the exchange of canonical histones with alternative variants to generate functionally specialized chromatin domains. Here we demonstrate that the alternative histone PfH2A.Z is associated with the epigenetic regulation of var genes. In many eukaryotic organisms the histone variant H2A.Z mediates an open chromatin structure at promoters and facilitates diverse levels of regulation, including transcriptional activation. Throughout the asexual, intraerythrocytic lifecycle of P. falciparum we found that the P. falciparum ortholog of H2A.Z (PfH2A.Z) colocalizes with histone modifications that are characteristic of transcriptionally-permissive euchromatin, but not with markers of heterochromatin. Consistent with this finding, antibodies to PfH2A.Z co-precipitate the permissive modification H3K4me3. By chromatin-immunoprecipitation we show that PfH2A.Z is enriched in nucleosomes around the transcription start site (TSS) in both transcriptionally active and silent stage-specific genes. In var genes, however, PfH2A.Z is enriched at the TSS only during active transcription in ring stage parasites. Thus, in contrast to other genes, temporal var gene regulation involves histone variant exchange at promoter nucleosomes. Sir2 histone deacetylases are important for var gene silencing and their yeast ortholog antagonises H2A.Z function in subtelomeric yeast genes. In immature P. falciparum parasites lacking Sir2A or Sir2B high var transcription levels correlate with enrichment of PfH2A.Z at the TSS. As Sir2A knock out parasites mature the var genes are silenced, but PfH2A.Z remains enriched at the TSS of var genes; in contrast, PfH2A.Z is lost from the TSS of de-repressed var genes in mature Sir2B knock out parasites. This result indicates that PfH2A.Z occupancy at the active var promoter is antagonized by PfSir2A during the intraerythrocytic life cycle. We conclude that PfH2A.Z contributes to the nucleosome architecture at promoters and is regulated dynamically in active var genes.

A Plasmodium Falciparum Bromodomain Protein Regulates Invasion Gene Expression

“…Recombinant GST fusion proteins of the PfBDP1 bromodomain and full-length PfHP1 were made and purified as described previously (Petter et al, 2011). Far-western blot was conducted as described (Wu et al, 2007) with minor modifications (see Supplemental Experimental Procedures).…”

“…This has been best studied in the var multigene family of immunodominant variant antigens (Duraisingh et al, 2005;Freitas-Junior et al, 2005;Petter et al, 2011;Volz et al, 2012). Differences in histone modifications that contribute to chromatin structure are also associated with the transcriptional activity of several invasion genes (Comeaux et al, 2011;Corté s et al, 2007;Crowley et al, 2011;Jiang et al, 2010).…”

A Plasmodium falciparum Histone Deacetylase Regulates Antigenic Variation and Gametocyte Conversion

“…Switches in expression of var genes and other virulence-associated, clonally variant multigene families are in part mediated by the presence of distinct histone modifications and variants (Lopez-Rubio et al, 2007; 2009; Petter et al, 2011). Active or silent chromatin states at individual loci within P. falciparum are written and maintained by the concerted actions of histone modifying enzymes such as the class III sirtuin histone deacetylases (HDACs) PfSir2a and PfSir2b (Duraisingh et al, 2005; Freitas-Junior et al, 2005; Tonkin et al, 2009) and the histone methyltransferases PfSET10 and PfSET2 (also known as PfSETvs) (Jiang et al, 2013; Volz et al, 2012).…”

Making a long story short: noncoding RNAs and chromosome change

“…UpsB-type var genes are located near these lncRNA-TARE, subtelomerically, and are subject to coordinated silencing and activity as part of antigenic variation in defense against the human immune response during malaria infection (reviewed in Cui and Miao, 2010). Gene regulation of the multigene var family is cell-cyle dependent, and is facilitated by epigenetic marks and nuclear repositioning (for example, Petter et al, 2011). LncRNA-TARE transcription is in sync with the chromatin-remodeling events that regulate var expression and thus, may facilitate the change in nucleosome architecture (Broadbent et al, 2011) or entire chromosome compartmentalization within the nucleus, pointing to a complex role for lncRNAs in both heterochromatin and nuclear architecture.…”