Fig. 1: RDProx-Mapping R-loop-proximal proteome on native chromatin.

a Schematic representation of the RDProx workflow for identification of R-loop-proximal proteins. HBD or HBD-WKK fused N-terminally to APEX2 were transiently expressed in light or heavy SILAC-labeled HEK293T cells. Biotinylation was induced upon the addition of 500 µM biotin–phenol for 2 h at 37 °C and 1 mM H₂O₂ for 2 min at room temperature. Samples were pooled after cell lysis and biotinylated proteins purified using NeutrAvidin beads. Denatured proteins were separated by SDS-PAGE and in-gel digested before LC-MS/MS analysis. b Volcano plot of protein groups identified by RDProx in n = 3 biologically independent experiments. Mean log₂ ratios of all replicates between HBD and HBD-WKK are plotted against the −log₁₀ FDR. The FDR and enrichment were calculated using Limma¹⁰³. Significantly enriched proteins are highlighted in blue (FDR < 0.01). Light blue indicates proteins in Tier 2 (300 proteins) above 2-fold change of the mean ratio and dark blue indicates proteins in Tier 1 (312 proteins) with a 4-fold change or higher. c Functional interaction network of proteins identified by RDProx. Genes were manually annotated based on literature and corresponding GO terms (Biological Process and Molecular Function). Clusters were generated based on the manual annotation. Edges between the nodes indicate interactions based on STRING with a confidence score equal or above 0.7.