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Execution of pluripotency requires progression from the naïve status represented by mouse embryonic stem cells (ESCs) to a state capacitated for lineage specification. This transition is coordinated at multiple levels. Non-coding RNAs may contribute to this regulatory orchestra. We identified a rodent-specific long non-coding RNA (lncRNA)  linc1281,  hereafter  Ephemeron  ( Eprn ), that modulates the dynamics of exit from naïve pluripotency.  Eprn  deletion delays the extinction of ESC identity, an effect associated with perduring Nanog expression. In the absence of  Eprn ,  Lin28a  expression is reduced which results in persistence of  let-7 microRNAs, and  the up-regulation of de novo methyltransferases Dnmt3a/b is delayed.  Dnmt3a/b  deletion retards ES cell transition, correlating with delayed  Nanog  promoter methylation and phenocopying loss of  Eprn  or  Lin28a . The connection from lncRNA to miRNA and DNA methylation facilitates the acute extinction of naïve pluripotency, a pre-requisite for rapid progression from preimplantation epiblast to gastrulation in rodents.  Eprn  illustrates how lncRNAs may introduce species-specific network modulations.

A lncRNA fine tunes the dynamics of a cell state transition involving Lin28 , let-7 and de novo DNA methylation