Fig. 2: Capture of RNA interactome by click chemistry upon acute NANOG degradation. | Nature Communications

Fig. 2: Capture of RNA interactome by click chemistry upon acute NANOG degradation.

From: Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts

Fig. 2: Capture of RNA interactome by click chemistry upon acute NANOG degradation.

a The schematic diagram showing capture of RNA interactome using click chemistry (RICK) in NANOG-AID cells. We treated the cells with IAA at different time points (i.e., 0 h, 2 h, 6 h), and incubated with 1 mM EU for 2 h. After 254 nm UV crosslinking, the cells were collected and lysed with lysis buffer. The resultant lysates were biotinylated and enriched with streptavidin agarose beads. The obtained RNA-protein complexes were digested for mass spectrometry. b Overlap between 786 RICK proteins and RBP2GO database54 (mouse, n = 2886). c Bar chart showing the number of 786 RICK proteins with classical RNA binding domains (left panel) and non-classical RNA binding domains (right panel). d Density plot showing the distribution of isoelectric point (pI) for 786 RICK proteins and control proteins (RICK searching proteins by MaxQuant, n = 3825). e Line plots showing the fold change (log2) dynamics of 786 RICK proteins at different time points compared to 0 h are represented, with each line corresponding to one protein. Solid lines, the mean values and the average trend of all proteins within the cluster. The 786 RICK proteins were categorized into three groups based on change trends: Increased (n = 89), Decreased (n = 106), and no significant change (n = 591). f GO analysis of increased proteins related to Fig. 2e (n = 89). g GO analysis of decreased proteins related to Fig. 2e (n = 106).

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