Fig. 1

Proteomic screening for Che-RBPs in three cell lines. a Schematic diagram showing the major steps of mass spectrometry (MS) screening and data analysis: proteins were collected from the soluble nuclear extract (SNE) and chromatin-pellet extract (CPE) fractions separately and identified by MS data analysis. b–d Sub-nuclear distribution of RBPs and TFs in THP-1 (b), K562 (c), and 293T (d) cells. The x-axis indicates the relative abundance of RBPs and TFs in the CPE fraction (protein area value in the CPE fraction/area value in the sum of SNE and CPE fractions). The y-axis shows the log2 (MS score + 1) of RBPs and TFs in the CPE fraction. The bubble size indicates the protein area value in the CPE fraction, and bubble color represents the different sub-nuclear location of RBPs and TFs. The MS score reflects reliability of identification. And the area value represents the relative abundance of protein. e Molecule function categories of common proteins located in the CPE fraction based on the DAVID database among three cell lines. Some proteins belonged to multiple categories and so were counted more than once. f Venn diagram showing the overlap between the common Che-RBPs expressed across three cell lines identified by the MS screening, known RBPs from RBP libraries (RBPDB and ATtRACT) and dsDNA-binding proteins reported in published studies. g Functional annotation and domain classification of the 52 common Che-RBPs. The network represents the affiliation of RBPs to related biological processes, based on gene ontology (GO) functional enrichment analysis, and the inner circle size indicates − log10 (P value) of GO functional enrichment analysis. The color of the outer ring corresponds to the different domains present in the RBPs. h Immuno-blot analysis of the distribution of the common Che-RBPs that were most abundant in the CPE fractions with/without RNase treatment