Trypanosome histone variants H3.V and H4.V promote nucleosome plasticity in repressed chromatin

Deák, G., Burdett, H., Watson, J.A., and Wilson, M.D.

By Cristina Cardenal Peralta, DRP-HCB Proteomics Core.

Chromatin can take two broad states: euchromatin, which comprises loosely packed DNA that is easily accessible to the transcription machinery, and heterochromatin, tightly packed DNA that is generally repressed and inaccessible. However, while this is also the case for the divergent parasite Trypanosoma brucei it lacks canonical heterochromatin. Instead trypanosomes use specialised histone variants H3.V and H4.V to promote repressive chromatin states. For example, H3.V and H4.V mark transcription termination regions. This alternative chromatin regulation is linked to parasite pathogenicity, as H3.V is enriched at silent VSG loci. VSG genes are central to the parasite’s virulence, as their tightly regulated expression allows T. brucei to evade the host immune response. T. brucei causes human and animal trypanosomiasis and is a model for other pathogenic kinetoplastids, such as T. cruzi and Leishmania.

In this study, researchers in the Wilson lab delved deeper into the structural features through which H3.V and H4.V promote repressive chromatin. Using cryo-EM, they visualised nucleosomes reconstituted with both variants and demonstrated that H3.V and H4.V can coexist within the same nucleosome. H3.V causes substantial structural alterations, particularly through its divergent N-terminal tail, whereas H4.V produces comparatively modest changes and slightly increases histone-octamer stability.

Surprisingly, reconstituted H3.V-containing nucleosomes exhibit highly splayed entry/exit DNA, despite their association with repressed chromatin. Cryo-EM and SAXS showed that this open nucleosome architecture is primarily driven by H3.V rather than H4.V. Importantly, increased DNA-end flexibility can facilitate alternative nucleosome-array packing and chromatin interactions, providing a potential mechanism by which structurally open nucleosomes contribute to a transcriptionally repressive, compacted chromatin environment. H3.V was therefore identified as the main driver of nucleosome plasticity, whereas H4.V had a more modest effect. 

These findings reveal that nucleosome openness and transcriptional accessibility are not necessarily synonymous, highlighting H3.V-driven nucleosome plasticity as a distinctive feature of repressive chromatin in T. brucei.

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