The human malaria parasite Plasmodium falciparum has a complex life cycle that includes various stages within the mosquito and within the human blood and liver. Thus, the parasite has to constantly adapt its gene expression profiles, which likely involves epigenetic modifications to its DNA. Now, Suman Kumar Dhar and colleagues (Bhowmick et al., 2020) investigate the regulation of P. falciparum GCN5, which acetylates H3K9 and H3K14, and thus promotes gene expression. Through immunoblotting, they find that GCN5 predominantly exists as various isoforms that are shorter than the full-length protein. Inhibition of cysteine proteases, however, increases the abundance of full-length GCN5, suggesting that the shorter isoforms arise from proteolytic cleavage. Moreover, the authors show that the short GCN5 isoforms predominantly localise to the nucleus during early and late stages of parasite development. In contrast, full-length GCN5 accumulates in the vicinity of the food vacuole of the parasite, suggesting that GCN5 cleavage might occur there. Finally, by using ChIP-seq, the authors demonstrate that GCN5 binds to genes involved in host cell entry and reprogramming. However, upon inhibition of GCN5 proteolytic processing, GCN5 binding to chromosomes and H3K9 acetylation at GCN5-binding sites are reduced. Collectively, these results indicate that the proteolytic processing of GCN5 promotes its localisation to the nucleus and its binding to target genes, thereby enhancing the transcription of genes that mediate successful infection of the host cell.