Fig. 4: Experimental validation of potential biomolecular condensates.

a Immunofluorescence images of mESC showing that SUPT6H (green) colocalizes with CTR9 (red) and SUPT5H (grey) in puncta. DNA was stained with DAPI (blue). This experimental result was consistent across two independent cell-seeding, fixation, and co-IF staining experiments (each contains three slides). Scale bar: 10 μm. b Line scans of the images of a cell co-stained for SUPT6H, CTR9 and SUPT5H, at the position depicted by the white line. The direction is from the green tick to the purple tick, and the two arrows refer to two representative puncta. FRAP experiments for SUPT6H (c), CTR9 (d) and SUPT5H (e). Left, representative images of the FRAP experiment. The white arrow refers to the punctum undergoing bleaching. Right, quantification of FRAP data for puncta of SUPT6H (n = 6), CTR9 (n = 5) and SUPT5H (n = 5). Puncta were photobleached at t = 0 s, and data were plot as mean ± standard error. Gene set enrichment analysis (GSEA)-like analyses for SUPT6H (f) and CTR9 (g), with all focus sites (CondSig-positive and -negative peaks of the CAP) were ranked by the log₂-transformed fold change in CUT&RUN signals and annotated against the set of CondSig-positive peaks. Fold changes were from 1,6-HD treatment versus wild type, and the pseudo count in fold change calculations was set to 0.1. The GSEA-like analyses were performed with Python package GSEApy (v1.1.2)⁶⁸. The enrichment score profile, the position of CondSig-positive peaks and fold change profiles were shown. The normalized enrichment score (NES) and false discovery rate (FDR) were labeled. h UCSC genome browser view of representative CondSig-positive sites. Signals represent RPM and the related loci were shaded in purple. Source data are provided as a Source Data file.