Time-course RNA-Seq analysis of spontaneously differentiating TE03 (I3) human embryonic stem cells (hESCs)

We used RNA-sequencing to explore the expression landscape of RBPs (RNA-binding proteins) during a time-course of spontaneously differentiating human embryonic stem cells (hESCs). RNA-Seq was performed on whole-cell extracts from TE03 (I3) hESCs harvested at six-time points (days 0, 15, 23, 30, 39, and 54), each with two biological replicates. This experiment accompanies our manuscript: "Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells". Abstract: "Embryonic stem cell (ESC) self-renewal and cell-fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that many RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, nearly 200 RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly bound by this factor. Using cross-linking and immunoprecipitation (CLIP-Seq), we discover that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Taken together, our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated".