Fluctuations in histone H4 isoforms during cellular reprogramming monitored by middle-down proteomics

Cellular reprogramming remodels the gene expression program by re-setting the epigenome of somatic cells into an embryonic-like pluripotent state. Post-translational modifications of histones play an important role in this process. Previously, we found by ChIP-seq widespread changes of specific histone H3 marks in two divergent reprogramming routes leading to alternative pluripotent sates . Here, using an unbiased middle-down proteomics approach we have identified 72 unique isoforms of histone H4 and quantified 56 of them in the same set of samples. We found substantial differences between somatic and late-phase reprogramming cells. Also, ESCs and iPSCs displayed higher levels of H4 acetylation and tri-methylation concomitantly with lower levels of mono- and di-methylation when compared to cells undergoing reprogramming. Our data shows that the epigenetic remodeling induced by the reprogramming process goes beyond histone H3 and reveals the importance of H4 modifications as well. The presented data is a valuable resource to study the epigenetic mechanisms involved in the acquisition of induced pluripotency. All MS data have been deposited in the ProteomeXchange with identifier PXD002062 (http://proteomecentral.proteomexchange.org/dataset/PXD002062).