After retinoic-acid-induced differentiation of ESCs, the ESC lincRNAs show temporal changes across the time course with ~75% showing a decrease in expression compared to untreated ESCs (Supplemental Figure 13, Supplemental Table 16). Notably, all of the lincRNAs shown to regulate pluripotency are down-regulated upon retinoic acid treatment (Supplemental Figure 13). Our results establish that lincRNAs are direct transcriptional targets of pluripotency-associated TFs and are dynamically expressed across differentiation. Collectively, these results demonstrate that lincRNAs are an important regulatory component within the ESC circuitry.
