Histone acetyltransferase Kat2a stabilises pluripotency with control of transcriptional heterogeneity

Cell fate transitions in mammalian stem cell systems have often been associated with transcriptional heterogeneity, however existing data have failed to establish a functional or mechanistic link between the two phenomena. Experiments in unicellular organisms support the notion that transcriptional heterogeneity can be used to facilitate adaptability to environmental changes and have identified conserved chromatin-associated factors that modulate levels of transcriptional noise. By inhibiting the paradigmatic histone acetyl-transferase, and candidate noise modulator, Kat2a (yeast orthologue Gcn5) in mouse embryonic stem cells, we show destabilisation of pluripotency-associated gene regulatory networks through increased global and locus-specific transcriptional heterogeneity. Functionally, network destabilisation associates with reduced pluripotency and accelerated mesendodermal differentiation, with increased probability of transitions into lineage commitment. Thus, we functionally link transcriptional heterogeneity to cell fate transitions through manipulation of the histone acetylation landscape of mouse embryonic stem cells and establish a general paradigm that could be exploited in other normal and malignant stem cell fate transitions. Differential chromatin H3K9 acetylation of mouse embryonic stem (ES) cells treated with Kat2/Gcn5 inhibitor MB-3 or vehicle (DMSO) for 48 hours in the presence of serum and leukaemia inhibitory factor (LIF). This series includes gene expression profiling of mouse embryonic stem (ES) cells treated with Kat2/Gcn5 inhibitor MB-3 or vehicle (DMSO).