LncRNA Osilr9 coordinates promoter DNA demethylation and the intrachromosomal loop structure required for maintaining stem cell pluripotency

Nuclear reprogramming of somatic cells into a pluripotent sta-tus has the potential to create patient-specific induced pluripo-tent stem cells for regenerative medicine. Currently, however, the epigenetic mechanisms underlying this pluripotent reprog-ramming are poorly understood. To delineate this epigenetic regulatory network, we utilized a chromatin RNA in situ reverse transcription sequencing (CRIST-seq) approach to identify long noncoding RNAs (lncRNAs) embedded in the 3-dimensional intrachromosomal architecture of stem cell core factor genes. By combining CRIST-seq and RNA sequencing, we identified Oct4-Sox2 interacting lncRNA 9 (Osilr9) as a pluripotency-associated lncRNA. Osilr9 expression was associated with the status of stem cell pluripotency in re-programming. Using short hairpin RNA (shRNA) knockdown, we showed that this lncRNA was required for the optimal main-tenance of stem cell pluripotency. Overexpression of Osilr9 induced robust activation of endogenous stem cell core factor genes in fibroblasts. Osilr9 participated in the formation of the intrachromosomal looping required for the maintenance of pluripotency. After binding to the Oct4 promoter, Osilr9 re-cruited the DNA demethylase ten-eleven translocation 1, lead-ing to promoter demethylation. These data demonstrate that Osilr9 is a critical chromatin epigenetic modulator that coordi-nates the promoter activity of core stem cell factor genes, high-lighting the critical role of pluripotency-associated lncRNAs in stem cell pluripotency and reprogramming.