Pluripotency-related, Valproic Acid (VPA)-induced Genome-wide Histone H3 Lysine 9 (H3K9) Acetylation Patterns in Embryonic Stem Cells

Background: Embryonic stem cell (ESC) chromatin is characterized by a unique set of histone modifications, including enrichment for H3K9ac. Recent studies suggest that HDAC inhibitors (HDACi) promote pluripotency. Results: Using H3K9ac ChIP-seq analyses and gene expression in E14 mouse ESCs before and after treatment with a low level of the HDACi valproic acid (VPA), we show that H3K9ac is enriched at gene promoters and is highly correlated with gene expression and with various genomic features, including different active histone marks and pluripotency-related transcription factors. Conclusion: This study provides insights into the genomic response of ESCs to low level HDACi, which leads to increased pluripotency. The results suggest that a mild (averaging less than 40%) but global change in the chromatin state is involved in increased pluripotency and that specific mechanisms operate selectively in bivalent genes to maintain constant H3K9ac levels. Our data support the notion that H3K9ac has an important role in ESC biology. Significance: Understanding the mechanisms that improve and support pluripotency of ESCs, such as the use of the HDAC inhibitor VPA, will promote intelligent manipulation of ESCs and expedite their use in the clinic.