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The regulation of variant gene expression in  Plasmodium falciparum  is still only partially understood. Regulation of  var  genes, the most studied gene family involved in antigenic variation, is orchestrated by a dynamic pattern of inherited chromatin states. Although recent evidence pointed to epigenetic regulation of transcribed and repressed  rif  loci, little is known about specific on/off associated histone modifications of individual  rif  genes. To investigate the chromatin marks for transcribed and repressed  rif  loci, we cultivated parasites and evaluated the transcriptional status of chosen  rif  targets by qRT-PCR and performed ChIP assays using H3K9ac and H3K9me3 antibodies. We then monitored changes in the epigenetic patterns in parasites after several reinvasions and also evaluated the “poised” mark in trophozoites and schizonts of the same erythrocytic cycle by ChIP using H3K4me2 specific antibodies. Our results show that H3K9 is acetylated in transcribed  rif  loci and trimethylated or even unmodified in repressed  rif  loci. These transcriptional and epigenetic states are inherited after several reinvasions. The poised modification H3K4me2 showed a tendency to be more present in loci in trophozoites that upon progression to schizonts strongly transcribe the respective locus. However, this effect was not consistently observed for all monitored loci. While our data show important similarities to  var  transcription-associated chromatin modifications, the observed swiftly occurring modifications at  rif  loci and the absence of H3K9 modification point to a different dynamic of recruitment of chromatin modifying enzymes.

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