Fig. 2

Large-scale sequencing of shared Che-RBPs. a Venn diagram showing the intersection between the common Che-RBPs and known hematopoiesis-related RBPs. Hematopoiesis-related RBPs were identified by literature and Gene Ontology database. b Immuno-blot validation of the distribution of hematopoietic Che-RBPs (hChe-RBPs) in the SNE and CPE fractions with/without RNase treatment. Immuno-blots of Histone H3 and SNRP70 were the same images from Fig. 1h since the same batch of SNE and CPE samples were used. c hChe-RBPs’ distribution on different gene types revealed by ChIP-seq (left panel) and CLIP-seq (right panel) datasets. d Enrichment of hChe-RBPs on different genomic regions. Upper panel: hChe-RBPs’ ChIP-seq signal distribution with human genomic intrinsic constitution as comparison. Lower panel: hChe-RBPs’ CLIP-seq signal distribution. e Comparison of occupied peak numbers (upper panel) and gene numbers (lower panel) between ChIP-seq and CLIP-seq datasets of indicated hChe-RBPs. f Heatmap showing the distribution ratios of CLIP-seq peaks neighboring ChIP-seq peaks of each hChe-RBP in different distance ranges on genome. g Comparison of hChe-RBP co-occupied genes from ChIP-seq and CLIP-seq datasets. The x-axis shows the Jaccard index of each hChe-RBP’s ChIP-seq and CLIP-seq occupied genes, with bubble size indicating co-occupied gene number. h Schematic diagram representing different interaction modes of hChe-RBPs to chromatin. i Heatmap presenting the occupation ratio of histone markers’ ChIP signals colocalized with hChe-RBPs’ ChIP peaks at promoter and gene body regions, respectively. j Upper panel: Odds ratio of differentially expressed genes (DEGs) determined by RNA-seq upon hChe-RBP knocking down on hChe-RBP-occupied versus non-occupied genes (*P value < 0.05, double-tail Fisher’s exact test). The odds ratio of IgG ChIP-seq dataset versus RNA-seq datasets upon hChe-RBPs knocking down was used as a randomized control. Lower panel: Formula of odds ratio. k GO functional enrichment analysis of hChe-RBP-occupied DEGs with scaled absolute value of log2FC