Extended Data Figure 2: RAP-MS identifies proteins that are known to directly interact with specific ncRNAs, and separates specific RNA interacting proteins from background proteins.
From: The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3
a, SILAC ratios of top proteins enriched in the RAP-MS U1 snRNA, 18S rRNA, and 45S pre-rRNA experiments. b, SILAC ratio plot of replicate captures of U1 snRNA versus 18S rRNA from one of two biologically independent label-swap experiments. Proteins associated with U1 are consistently found in U1 samples, both light and heavy labelled (top right quadrant), and proteins specifically associated with 18S are consistently identified in 18S, both light and heavy (lower left quadrant). Background contaminant proteins have low enrichments (centre of panel) or are consistently found in the light channel and do not replicate between experiments (that is, keratin, streptavidin). c, SILAC ratio plot of replicate captures of U1 snRNA versus 45S pre-rRNA from one label-swap experiment. Proteins that are known to associate with 45S pre-rRNA are consistently identified in 45S captures.
