Cystatin B-deficiency triggers ectopic histone H3 tail cleavage during neurogenesis

Cystatin B (CSTB) acts as an inhibitor of cysteine proteases of the cathepsin family and loss-of-function mutations result in human brain diseases with a genotype-phenotype correlation. In the most severe case, CSTB-deficiency disrupts brain development, and yet the molecular basis of this mechanism is missing. Here, we establish CSTB as a regulator of chromatin structure during neural stem cell renewal and differentiation. Murine neural precursor cells (NPCs) undergo transient proteolytic cleavage of the N-terminal histone H3 tail by cathepsins B and L upon induction of differentiation into neurons and glia. In contrast, CSTB-deficiency triggers premature H3 tail cleavage in undifferentiated self-renewing NPCs and sustained H3 tail proteolysis in differentiating neural cells. This leads to significant transcriptional changes in NPCs, particularly of nuclear-encoded mitochondrial genes. In turn, these transcriptional alterations impair the enhanced mitochondrial respiration that is induced upon neural stem cell differentiation. Collectively, our findings reveal the basis of epigenetic regulation in the molecular pathogenesis of CSTB deficiency. [Display omitted] •Neural stem cell differentiation involves histone H3 tail proteolysis.•Histone H3 cleavage is most prevalent in postmitotic neurons.•Cystatin B regulates histone H3 cleavage by inhibition of cysteine cathepsins B and L.•Absence of cystatin B causes ectopic histone H3 cleavage in neural precursors.•Absence of cystatin B leads to mitochondrial dysfunction upon differentiation.