Knockdown of Plasmodium falciparum Jumonji C2 histone demethylase leads to a global perturbance of gene expression but does not alter var gene transcription
The gene expression of the human malaria parasite Plasmodium falciparum is dynamically controlled by multiple factors and events including chromatin modifiers. Here, we addressed the effect of a temporary knockdown of the non-essential putative chromatin modifier P. falciparum JumonjiC2 histone demethylase (JmjC2) during asexual blood stages. While ribozyme-mediated transcript-knockdown of PfJmjC2 resulted in the differential transcription of many genes culminating in a delay of cycle progression, ChIPseq analysis pointed to only a few loci with which JmjC2 seemed to associate, including variant gene encoding loci. Knockdown also altered the methylation and acetylation patterns of H3K4 and H3K9, important for global gene regulation, including variant/virulence-associated gene families. However, RT-qPCR based analysis of variant (var) gene transcription of knocked-down or control parasites showed only a partial decrease of dominant var transcripts without changing variant gene transcription patterns. Collectively, JmjC2 appears to be an important, yet dispensable player at least during intraerythrocytic development. The differential transcription of many genes that results from the knockdown of JmjC2 probably reflects a generalized temporary delay in cycle progression. Overall design: RNA was Trizol-extracted from synchronized triplicate parasite cultures which were treated or not with glucosamine to effect a ribozyme-mediated knockdown of the histone modifier JmjC2. RNA was then converted in cDNA and used for library construction following the Illumina protocol.