Long non-coding RNAs (lncRNAs) act as epigenetic regulators of gene expression. Oct4 is the only indispensible factor for iPS cell generation. Here we present a panel of new mouse Oct4 pseudogenes and demonstrate that the X-linked Oct4 pseudogene Oct4P4 critically impacts mouse embryonic stem cells self-renewal.

We have identified four additional candidate pseudogenes that show high homology to portions of the open reading frame and untranslated regions of Oct4. Among them, Oct4P4 lncRNA forms a complex with the SUV39H1 HMTase to direct the imposition of H3K9me3 and HP1a to the promoter of the ancestral Oct4 gene, located on chromosome 17, leading to gene silencing and reduced mESC self-renewal.

Depleting Oct4P4 from differentiated pMEFs results in the re-activation of basic features of mESC pluripotency, such as self-renewal transcription factor expression. Targeting Oct4P4 expression in primary mouse embryonic fibroblasts causes the re-acquisition of self-renewing features of mESC.

In summary, we demonstrate that Oct4P4 lncRNA plays an important role in inducing and maintaining silencing of the Oct4 gene in differentiating mESCs.  The Oct4P4 lncRNA represents the first example for a crucial role of a vertebrate pseudogene derived sense lncRNAs in directing chromatin-modifying activities to the promoter of its ancestral gene.