Fig. 6: Association of PCGF1 with the replication fork limits access of chromatin remodelers. | Nature Communications

Fig. 6: Association of PCGF1 with the replication fork limits access of chromatin remodelers.

From: PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment

Fig. 6

a A scatterplot view for PCGF1 interactors in IdHPCs. The X and Y axes denote log2 signal intensities of proteins in the mock immunoprecipitation (the negative control: NC) and log2 ratios of the label-free quantification intensities of immunoprecipitated materials over the negative control (log2 FC), respectively. Orange font denotes proteins with log2 FC > 0.3. Data represent the average of two independent experiments. b Proximity Ligation Assay (PLA) revealed association between 3xFLAG-tagged PCGF1 and EdU-labeled nascent DNA. Pcgf1-KO IdHPCs with or without exogenous Pcgf1 were used. PLA, red; DAPI, blue. Representative data from biological triplicates are shown. c A heatmap of ChIP-seq and iPOND-ChIP signals for endogenous TY1-PCGF1 across TSS ( ± 10 kb) in IdHPCs. Data represent the average of two independent experiments. d Scatterplot of iPOND-MS in control and Pcgf1-KO IdHPCs. The X and Y axes indicate log2 intensities of the control and log2 ratios of signal intensity of Pcgf1-KO over the control, respectively. Representative data from two independent biological duplicates are shown. Blue and red fonts, respectively, indicates proteins with log2 FC < −0.4 and log2 FC > 0.4. e Suppression of BRG1 overloading to nascent DNA by PCGF1 in IdHPCs. iPOND materials without (Nascent) or with thymidine chase (Mature) were examined by respective immunoblotting. Representative data from biological duplicates are shown. f ChIP-qPCR for BRG1 in control and Pcgf1-KO IdHPCs. Data represent mean ± SD of three independent experiments. g, h Destabilization of nucleosomes on nascent DNA g and steady state DNA h around TSS in Pcgf1-KO IdHPCs and its partial restoration by drug-induced degradation of BRG1. g Results of iPOND-MNase-Seq in respective conditions. h Results of MNase-Seq. Data are the average of two independent experiments. i Partial restoration of H3K27me3 destabilization around the TSS of selected C1 genes in Pcgf1-KO IdHPCs by degradation of BRG1 revealed by ChIP-qPCR. Data represent mean ± SD of four independent experiments. j Partial restoration of Hmga2 up-regulation in Pcgf1-KO IdHPCs by BRG1 depletion revealed by qRT-PCR. Data represent mean ± SD of three independent experiments. p-values between the control and Pcgf1-KO calculated with the Student’s two-sided t test are shown.

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