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

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, resulting in persistence of let-7, and 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. Overall design: RNA Seq expression profiling mouse ES cells was conducted to compared the expression of transcripts in mES wild-type (WT) and mES cells with knockout of the lncRNA ephemeron (KO). Cells were grown in PD/LIF medium, or following 8 hours withdrawal from PD/LIF. All conditions were conducted using three indepedent cell lines served as biological triplicates. ChIRP seq of ephemeron targets was also conducted in WT and KO cells (in duplicate), along with WT and KO input controls and 7SK ChIRP seq.