Fig. 3: Polysome profiling and sequencing and SuNSET assay suggests MSI1 is aberrantly impeding the association of transcripts with ribosomes with subsequent whole shot gun proteomic analysis identifying downregulation of proteins associated with cancer aggressiveness. | Nature Communications

Fig. 3: Polysome profiling and sequencing and SuNSET assay suggests MSI1 is aberrantly impeding the association of transcripts with ribosomes with subsequent whole shot gun proteomic analysis identifying downregulation of proteins associated with cancer aggressiveness.

From: Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma

Fig. 3

a Schematic of experimental plan to investigate the ribosome associated fraction of mRNA and validation of global translational process with SuNSET assay, b Polysome profile of control vs shMSI1 SU_MB002 illustrating an increased mRNA polysome associated fraction in shMSI1 inhibited samples, c Polysome-seq identifies key cancer associated genes that are down regulated in the polysome fractions after shMSI1 inhibition in SU_MB002, d SuNSET assay after normalization shows a trend towards increased nascent polypeptide production in shMSI1 inhibited samples in SU_MB002 and NSC201, e Schematic of experimental plan to quantitatively investigate the proteomic landscape after shMSI1 inhibition, f MaxQUANT and PERSEUS analysis of TMT-MS data showing 350 significantly differentially abundant proteins in the shMSI1 samples compared to the control (Significance B < 0.05), g Volcano plot with annotation of key genes that are up and down regulated at the proteomic level with ~50% inhibition of the MSI1 protein, h PSEA analysis identifying downregulation of proteins associated with cancer aggressiveness in green, and upregulation of genes associated with neuronal differentiation and DNA fragmentation in red (log2p > 1).

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