Small-RNA Sequencing Highlights Major MicroRNAs Promoting Ground State Pluripotency

Embryonic stem cells (ESCs) are characterized by unlimited self-renewal and multi-lineage differentiation. They have numerous applications in studying embryonic development, drug screening, disease modeling, and cell therapy. Self-renewal and multi-lineage differentiation potential of ESCs are orchestrated by an integrated network of biomolecules including transcription factors and non-coding RNAs such as microRNAs. Here, we show that microRNAs are differentially expressed in ground state ESCs compared to serum cells. We find that the imprinted Dlk1-Dio3 locus expresses the majority of ground state-specific microRNAs. Computational analysis predicts that ground state microRNAs repress numerous differentiation pathways. Functional analysis reveals that ground state microRNAs embedded in the Dlk1-Dio3 locus promote pluripotency via inhibition of multi-lineage differentiation and stimulation of self-renewal. Taken together, we demonstrate that microRNAs are differentially expressed in different pluripotency contexts and that ground state microRNAs promote pluripotency by stimulating diverse aspects of self-renewal and inhibiting differentiation.