The establishment and maintenance of highly specialised cell lineages is fundamental to the
development of multicellular organisms. Cell identity is determined by specific transcriptional profiles,
which are mediated by sequence-specific, chromatin-based and post-transcriptional mechanisms of
gene regulation. Changes in cell morphology and chromatin structure which occur during the cell
cycle present a challenge to the maintenance of lineage-specific gene expression profiles. This study
investigates the role of post-transcriptional regulation by microRNAs in stabilising cell-specific gene
expression through the process of cell growth and division. Data presented here show that
microRNAs are inherited through mitosis in mammalian cells, and are capable of regulating target
gene expression in recipient daughter cells. Genome-wide expression analysis indicates that key
developmentally regulated genes marked by a bivalent chromatin signature are globally upregulated
in microRNA-deficient ES cells. Binding sites for ES cell-specific microRNAs are significantly enriched in the 3'UTR of these transcripts compared to the rest of the transcriptome, strongly suggesting that
microRNAs contribute to maintenance of ES cell identity by co-ordinately regulating multiple lineage
inappropriate genes. Finally, analysis of the expression of validated microRNA targets and bivalent
genes throughout the cell cycle shows that transcripts from these genes accumulate in G2/M to a
greater extent in microRNA-deficient ES cells than in wildtype cells. Taken together, data presented in
this study support a role for microRNAs in regulation of lineage-specific gene expression through the
cell cycle.