To determine if lincRNA expression is functionally regulated by the pluripotency-associated TFs, we used shRNAs to knock down the expression of 5 of the 9 pluripotency-associated TF genes for which we could obtain validated hairpins and profiled the resulting changes in lincRNA expression after 4 days. Upon knockdown of a TF, ~50% of lincRNAs genes whose promoters are bound by the TF exhibit expression changes (Figure 4a); this proportion is comparable to that seen for protein-coding genes whose promoters are bound by the TF (Supplemental Figure 12). The strong but imperfect correlation between TF-binding and effect of TF-knockdown is consistent with previous observations39 and may reflect regulatory redundancy in the pluripotency network40. In addition, we profiled the knockdown of an additional 7 pluripotency-associated transcription factors (including Esrrb, Zfp42, and Stat3). Altogether, for ~60% of the ESC lincRNAs, we identified a significant downregulation upon knockdown of one of these 11 TFs (Figure 4b, Supplemental Table 15).
