Much has been learned about the mechanisms of action of pluripotency factors Oct4 and Sox2. However, as with other regulators of cell identity, little is known about the impact of disrupting their binding motifs in a native environment or the characteristics of genes they regulate. By quantitatively examining dynamic ranges of gene expression instead of focusing on conventional measures of differential expression, we found that Oct4 and Sox2 enhancer binding is strongly enriched near genes subject to large dynamic ranges of expression among cell types, with binding sites near these genes usually within superenhancers. Mutagenesis of representative Oct4:Sox2 motifs near such active, dynamically regulated genes revealed critical roles in transcriptional activation during reprogramming, with more limited roles in transcriptional maintenance in the pluripotent state. Furthermore, representative motifs near silent genes were critical for establishing but not maintaining the fully silent state, while genes whose transcript levels varied by smaller magnitudes among cell types were unaffected by nearby Oct4:Sox2 motifs. These results suggest that Oct4 and Sox2 directly establish both active and silent transcriptional states in pluripotent cells at a large number of genes subject to dynamic regulation during mammalian development, but are less important than expected for maintaining transcriptional states.

In eukaryotic organisms, histone posttranslational modifications (PTMs) are indispensable for their role in maintaining cellular physiology, often through their mediation of chromatin-related processes such as transcription. Targeted investigations of this ever expanding network of chemical moieties continue to reveal genetic, biochemical, and cellular nuances of this complex landscape. In this study, we present our findings on a novel class of histone PTMs: Serine, Threonine, and Tyrosine O-acetylation. We have combined highly sensitive nano-LC-MS/MS experiments and immunodetection assays to identify and validate these unique marks found only on histone H3. Mass spectrometry experiments have determined that several of these O-acetylation marks are conserved in many species, ranging from yeast to human. Additionally, our investigations reveal that histone H3 serine 10 acetylation (H3S10ac) is potentially linked to cell cycle progression and cellular pluripotency. Here, we provide a glimpse into the functional implications of this H3-specific histone mark, which may be of high value for further studies of chromatin.