Here we show that knockdown of the vast majority of ESC-expressed lincRNAs has a strong effect on gene expression patterns in ESCs, of comparable magnitude to that seen for the well-known ESC regulatory proteins. We identify dozens of lincRNAs that upon loss-of-function cause an exit from the pluripotent state and dozens of additional lincRNAs that, while not essential for the maintenance of pluripotency, act to repress lineage-specific gene expression programs in ESCs. We integrate the lincRNAs into the molecular circuitry of ESCs by demonstrating that most lincRNAs are directly regulated by critical pluripotency-associated transcription factors and ~30% of lincRNAs physically interact with specific chromatin regulatory proteins to affect gene expression. Together, these results demonstrate a regulatory network in ESCs whereby transcription factors directly regulate the expression of lincRNA genes, many of which can physically interact with chromatin proteins, affect gene expression programs, and maintain the ESC state.
