Quantification of the effect of site-specific histone acetylation on chromatin remodeling rate

Eukaryotic transcription is epigenetically regulated by chromatin structure and post-translational modifications (PTMs). For example, lysine acetylation in histone H4 is correlated with activation of RNA polymerase I-, II-, and III-driven transcription from chromatin templates, which requires prior chromatin remodeling. However, quantitative understanding of the contribution of particular PTM states to the sequential steps of eukaryotic transcription has been hampered partially because reconstitution of a chromatin template with designed PTMs is difficult. In this study, we reconstituted a di-nucleosome with site-specifically acetylated or unmodified histone H4, which contained two copies of the Xenopus somatic 5S rRNA gene with addition of a unique sequence detectable by hybridization-assisted fluorescence correlation spectroscopy. Using a Xenopus oocyte nuclear extract, we analyzed the time course of accumulation of nascent 5S rRNA transcripts generated on chromatin templates in vitro . Our mathematical model and fitting analyses revealed that tetra-acetylation of histone H4 at K5/K8/K12/K16 increases the chromatin remodeling rate ~3-fold in comparison with the absence of acetylation. We provide a mathematical model for quantitative evaluation of the contribution of epigenetic modifications to chromatin transcription.