Abstract
Post‐translational modifications of histone H3 N‐terminal tails are key epigenetic regulators of virulence gene expression and sexual commitment in the human malaria parasite Plasmodium falciparum. Here, we identify proteolytic clipping of the N‐terminal tail of nucleosome‐associated histone H3 at amino acid position 21 as a new chromatin modification. A cathepsin C‐like proteolytic clipping activity is observed in nuclear parasite extracts. Notably, an ectopically expressed version of clipped histone H3, PfH3p‐HA, is targeted to the nucleus and integrates into mononucleosomes. Furthermore, chromatin immunoprecipitation and next‐generation sequencing analysis identified PfH3p‐HA as being highly enriched in the upstream region of six genes that play a key role in DNA replication and repair: In these genes, PfH3p‐HA demarcates a specific 1.5 kb chromatin island adjacent to the open reading frame. Our results indicate that, in P. falciparum, the process of histone clipping may precede chromatin integration hinting at preferential targeting of pre‐assembled PfH3p‐containing nucleosomes to specific genomic regions. The discovery of a protease‐directed mode of chromatin organization in P. falciparum opens up new avenues to develop new anti‐malarials.
Highlights
Post-translational modifications of histone H3 N-terminal tails are key epigenetic regulators of virulence gene expression and sexual commitment in the human malaria parasite Plasmodium falciparum
We identified for the first time in a protozoan pathogen the clipping of the N-terminal region of histone H3 at amino acid 21, deleting the N-terminal tail from amino acids 1–21: This region is highly methylated and acetylated at positions lysine 4, lysine 9, lysine 14, and lysine 18, with particular marks being associated with transcriptional activation (H3K4me3 and H3K9ac) and others with regulation of variegated gene expression (H3K9me3), including of virulence genes involved in immune evasion and genes regulating sexual commitment [4,5,7,15,17, 23,24]
To determine whether histone proteolysis occurs during P. falciparum intra-erythrocytic development, we prepared nuclear and cytoplasmic extracts of 3D7 parasites synchronized at the ring [6– 10 hours post-invasion], trophozoite (26–30 hpi), or schizont (36–40 hpi) stages, and analyzed them by immunoblotting with antibodies targeting the C-terminus of histone H3 or histone H4 (Fig 1A)
Summary
Post-translational modifications of histone H3 N-terminal tails are key epigenetic regulators of virulence gene expression and sexual commitment in the human malaria parasite Plasmodium falciparum. We identify proteolytic clipping of the N-terminal tail of nucleosome-associated histone H3 at amino acid position 21 as a new chromatin modification. An ectopically expressed version of clipped histone H3, PfH3p-HA, is targeted to the nucleus and integrates into mononucleosomes. Chromatin immunoprecipitation and next-generation sequencing analysis identified PfH3p-HA as being highly enriched in the upstream region of six genes that play a key role in DNA replication and repair: In these genes, PfH3p-HA demarcates a specific 1.5 kb chromatin island adjacent to the open reading frame. In P. falciparum, the process of histone clipping may precede chromatin integration hinting at preferential targeting of pre-assembled PfH3p-containing nucleosomes to specific genomic regions. The discovery of a proteasedirected mode of chromatin organization in P. falciparum opens up new avenues to develop new anti-malarials
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