Although thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized, leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem (ES) cells and characterized the effects on gene expression. Here we show that knockdown of lincRNAs has major consequences on gene expression patterns, comparable to knockdown of well-known ES cell regulators. Notably, lincRNAs primarily affect gene expression in trans. Knockdown of dozens of lincRNAs causes either exit from the pluripotent state or upregulation of lineage commitment programs. We integrate lincRNAs into the molecular circuitry of ES cells and show that lincRNA genes are regulated by key transcription factors and that lincRNA transcripts bind to multiple chromatin regulatory proteins to affect shared gene expression programs. Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ES cell state. Mammalian genomes encode many classes of RNA that do not correspond to messenger (protein-coding) RNAs, transfer RNAs or ribosomal RNAs. Whether these non-coding RNAs have a function, and what that might be, remain outstanding questions. Lander and colleagues have performed a systematic loss-of-function analysis of the long intergenic non-coding RNAs (lincRNAs) in mouse embryonic stem cells. Some of these are found to affect known regulators of the pluripotent state, indicating that they are functional. This work sets the stage for experiments to determine the precise mechanistic roles of lincRNAs.

lincRNAs act in the circuitry controlling pluripotency and differentiation