ena-STUDY-TECHNION-ISRAEL INSTITUTE OF TECHNOLOGY-03-04-2021-18:34:12:768-621
RNA-sequencing analysis comparing gene expression between TE03 (I3) human embryonic stem cells (hESCs) and human foreskin fibroblasts (HFFs)
In this experiment, we performed RNA-sequencing to identify differentially expressed RBPs (RNA-binding proteins) between undifferentiated TE03 (I3) human embryonic stem cells (hESCs) and fully differentiated human foreskin fibroblasts (HFFs). 2102Ep embryonal carcinoma (EC) cells were used as a reference for pluripotent cells. Each library was sequenced on two lanes on an Illumina HiSeq 2500, yielding an average of 21 M single-end (SE) reads of length 101-bp. This data accompanies the 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".
In this experiment, we performed RNA-sequencing to identify differentially expressed RBPs (RNA-binding proteins) between undifferentiated TE03 (I3) human embryonic stem cells (hESCs) and fully differentiated human foreskin fibroblasts (HFFs). 2102Ep embryonal carcinoma (EC) cells were used as a reference for pluripotent cells. Each library was sequenced on two lanes on an Illumina HiSeq 2500, yielding an average of 21 M single-end (SE) reads of length 101-bp. This data accompanies the 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".