Extended Data Fig. 4: Cell-context-dependent RDAP assemblies of 13 RBPs.
From: irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNA
(a) Scatter plots indicate log2FC values in HEK293T and HepG2 of differentially enriched RDAPs with the 13 RBPs after comparing RNP subzones #2 and #3 against #1 (left and right plots, respectively). Green and blue dots: low and high-molecular-mass (MM) RDAPs; dark red dots: ambivalent distributed RDAPs between HEK293T and HepG2; orange circle: RDAPs with significant differences in TMT intensity distribution across the RNP subzones between HEK293T and HepG2. (b) Lines indicate the cumulative fraction of MM of low and high-MM RDAPs and background proteins in HEK293T (left) and HepG2 (right). Black line: background proteins; green and blue lines: high and low-MM RDAPs in HEK293T and HepG2. P-values between high and low-MM RDAPs against the background in each cell line were determined by a two-sided Kolmogorov-Smirnov test. (c) Schematics of the RDAP categorization in the different RNP subzones, according to slope values calculated between the RNP subzone #1-3 intensity ratios. (d) Representative nitrocellulose image of n = 3 biologically independent experiments indicates the infrared signal of sequential irCLIP-RNP immunoprecipitation of NONO followed by the RDAPs HNRNPC, HNRNPM, HNRNPU, NONO, SFPQ, and ABCF1 as well as the negative control proteins EIF5B and THOC2. L: ladder.
