Transcriptional memory and switching in the Plasmodium falciparum rif gene family

Abstract

The human malaria parasite Plasmodium falciparum expresses erythrocyte-surface directed variant antigens which are important virulence factors. Many are transcribed from multigene families and presumably their mode of expression is strictly controlled to guarantee immune evasion in the human host. In order to elucidate the dynamics of rif transcription and to investigate if rif switching is comparable to var switching we monitored rif variant gene expression in parasites with different cytoadhesive properties as well as after a number of reinvasions. We found identical transcripts in parasite lines with different adhesive phenotypes suggesting that rif genes do not have a critical role in determining the cytoadhesion specificity of infected erythrocytes. We show for the first time that rif genes may show a conserved mode of transcription, maintaining the previously dominant rif transcript in subsequent reinvasions, but also observed rapid switching at rates up to 45% per generation, much higher than for the var gene family.

Dynamic Activation and Repression of the Plasmodium falciparum rif Gene Family and Their Relation to Chromatin Modification

“…Our data suggest that both loci PFI0025c and PFD0070c may also be regulated epigenetically at the studied time points in sporozoites and gametocytes. Our experiments did not show any connection of rif transcription and cytoadherence patterns, since the transcripts found in the re-selected parasite line showed transcripts differing from those identified in our previous study (Figure 2 and [5]). This view is also supported by a recently published microarray-based analysis [25].…”

“…In order to establish if the dynamics of activation and repression of rif loci are associated with the same epigenetic landmarks as var loci, we first performed a qRT-PCR-based rif transcript analysis in parasites previously selected for cytoadherence in CHO-CD36, since in this phenotype a number of rif loci were found active with rapid switching after a small number of reinvasions and given the large number of rif genes the analysis was restricted to these loci [5]. We monitored the transcriptional status of this set of rif genes after 10 and 20 reinvasions after the last panning procedure.…”

“…It is possible that unmodified H3K9 residues are associated to an almost permanently silent locus while H3K9me3 loci were recently switched off or may become switched on. Further, the turnover dynamics are probably faster [5] than for var loci. Additional studies targeting the exact chromatin modifications at other histone residues [30] or at H4 [18] comparing active or silent variant gene loci are clearly necessary in order to elucidate the mechanics of recruiting transcription factors to the respective sites.…”

“…Since the selective upregulation of rif genes by phenotypic selection is not yet possible as it is for var genes e.g. [21], [14], we took advantage of the accelerated switching of rif genes and the frequent transcriptional activity of the herein tested loci [5] and monitored parasite cultures over 10 reinvasion cycles. Over the time, “on” and “off” states were observed in a number of loci and permitted the measurement of the underlying histone modifications.…”

“…Recently, we [5] and others [6] have characterized the transcriptional profile of this family, showing that i) particular, sometimes identical transcripts are expressed in different adhesive phenotypes and ii) that rif transcription switches apparently faster than transcription of var genes, at least in vitro . Similar to var genes, rif gene transcription and silencing is dependent on the histone deacetylase PfSir2A [7] and genome-wide chromatin immunoprecipitation experiments have shown that silent rif gene loci are associated to histone 3 lysine 9 trimethylation as are other virulence-associated multigene families [8], [9].…”