Identification of histone H3 clipping activity in human embryonic stem cells

•Histone H3 proteolysis is shown for the first time in human embryonic stem cells.•This clipping is visualized in both pluripotent and differentiating conditions.•Different cleavage time-patterns are seen dependent on the culture conditions.•Three possible histone H3 target sites were identified.•This epigenetic modification is catalyzed by a serine protease.

Posttranslational histone modifications are essential features in epigenetic regulatory networks. One of these modifications has remained largely understudied: regulated histone proteolysis. In analogy to the histone H3 clipping during early mouse embryonic stem cell differentiation, we report for the first time that also in human embryonic stem cells this phenomenon takes place in the two different analyzed cell lines. Employing complementary techniques, different cleavage sites could be identified, namely A21, R26 and residue 31. The enzyme responsible for this cleavage is found to be a serine protease. The formation of cleaved H3 follows a considerably variable pattern, depending on the timeframe, culture conditions and culture media applied. Contrary to earlier findings on H3 clipping, our results disconnect the link between declining Oct4 expression and H3 cleavage.