Fig. 8: Identification of PU.1 proximal proteins using BioID.

a Schematic of the experimental setup. b Volcano plot illustrating proteins significantly enriched in PU.1-BirA-mRNA-transfected CTV-1 cells compared with NLS-BirA-mRNA-transfected control cells. Blue dots represent proteins with FDR < 0.05 and log fold change (logFC) > 2. Only PU.1-specific proteins of GO terms for chromatin organization and interesting transcriptional regulators are highlighted. c STRING analysis illustrating the functional protein association network. The network view summarizes predicted associations for proteins significantly enriched in the PU.1-BioID. The network nodes represent the proteins, the edges represent predicted functional associations. Only connected nodes are shown. d Dot plots showing the enrichment of peptides (ratios of log₂-transformed normalized iBAQ values) representing the indicated SWI/SNF components (PU.1/SPI1 is shown as a control) in BioIDs from PU.1-BirA vs. NLS-BirA (control), ΔQ-BirA, or ΔA-BirA-mRNA-transfected CTV-1 cells (***P < 0.001; **P < 0.01; *P < 0.05; paired t-test, permutation-based correction). e Immunoblotting of αFLAG mAb immunoprecipitations (5 h after electroporation, IP 5 h), along with corresponding input lysates of control (mock), PU.1, ΔQ, ΔA, and BirA-mRNA-transfected cells using the indicated antibodies. f IGV genome browser tracks for the GSN locus showing SMARCA4 (BRG1) and PU.1 ChIP-seq, as well as ATAC-seq coverage in control (mutPU.1, gray–green)-, PU.1 (blue)-, ΔQ mutant (green)-, and ΔA mutant (lightbrown)-expressing cells. g Distribution of the PU.1 ChIP-seq, ATAC-seq signal, and SMARCA4 (BRG1) ChIP-seq signals in control (mutPU.1), PU.1, ΔQ, and ΔA mRNA-transfected cells across the 45 K clustered PU.1-binding sites, as well as the disappearing ~3 K sites that were accessible prior to PU.1 induction. b–e, g Source data are provided as a Source Data file.