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E-MEXP-2115

ABSTRACT: Transcription profiling by array of CDC7 siRNA knockdown in human embryonic lung fibroblasts

PROVIDER: E-MEXP-2115 | ExpressionAtlas | 2025-01-22

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MEXP-2115-analysis-methods.tsv	Tabular
	E-MEXP-2115-atlasExperimentSummary.Rdata	Rdata
	E-MEXP-2115-configuration.xml	Xml
	E-MEXP-2115-percentile-ranks.tsv	Tabular
	E-MEXP-2115.condensed-sdrf.tsv	Tabular

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Project description:Here, we used high-resolution mass spectrometry to identify differentially expressed RNA-binding proteins (RBPs) between TE03 (I3) human embryonic stem cells (hESCs) and human foreskin fibroblasts (HFFs). 2102Ep embryonal carcinoma (EC) cells were used as a reference for pluripotent cells. 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 directly bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during exit from pluripotency and early lineage specification. Moreover, we show that nearly 200 RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly bound by this factor. Intriguingly, over 20 percent of the proteins detected in our study are putative DNA- and RNA-binding proteins (DRBPs), among them key transcription factors (TFs). Using fluorescently labeled RNA and seCLIP (single-end enhanced crosslinking and immunoprecipitation) experiments, we discover that the pluripotency-associated STAT3 and OCT4 TFs interact with RNA in hESCs and confirm the direct 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, reinforcing the importance of post-transcriptional regulation in stem cell biology".

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