Extended Data Fig. 5: YBX1 interaction with spliceosome components and validation of YBX1-MAPK1 partnership.

a, Study design of mouse YBX1 interactome. n = 4 biological replicates and YBX1 interactome analysed in LC-MS/MS. Using Perseus, samples were filtered for a minimum of three valid values in at least one group. In total 614 high confident interactors of YBX1 were identified (t-test with permutation-based FDR < 0.05) with 260 JAK2VF-specific interactors. b, Network representation of YBX1 interacting spliceosomal proteins in JAK2VF cells. The size and colour of the node indicates the abundance of the corresponding proteins (z-scored protein intensity) and the edges are connected by STRING database interactions. c, List of significant YBX1-interacting spliceosomal proteins presented according to their spliceosome complex. d, Spliceosome proteins interacting with YBX1 participate in spliceosome assembly reaction in a stepwise manner to excise intronic sequences from immature mRNA to form a mature mRNA. e, Network representation of YBX1 interactome (regulated in both JAK2WT and JAK2VF) based on annotation keywords. The keywords are highlighted in colours according to the protein function. n = 4 biological replicates, t-test with permutation-based FDR < 0.05. f, Scatter plot of YBX1 interactome in JAK2VF vs control. YBX1 interactome is enriched for GO term mRNA splicing factor (green) and Ribonucleoproteins (blue) assessed by Fisher’s exact test. Fold enrichment of YBX1 and MAPK1 in JAK2VF cells compared to IgG control plotted against –log₁₀ Student t-test P value. g, Scatter plot of YBX1 interactome in DMSO vs JAK inhibitor (RUX 0.5 μM, 4 h)-treated JAK2VF cells. Fold enrichment of MAPK1 in DMSO vs JAK inhibitor plotted against –log₁₀ Student’s t-test P value. h, Immunoprecipitation of YBX1 from mouse JAK2VF cells ± RUX, 0.5 –μM for 4 h and analysed for interaction with MAPK1 by western blot analysis using ERK1/2 antibody. Representative images from n = 3 biological experiments.

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