Fig. 7From: Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecturePol III depletion increased nucleosome occupancy as an underlying mechanism related to slow down the Pol II transcription rate. A Mean coverage profiles for the ratio of PRO-Seq over Pol II ChIP-Seq signal (PRO-Seq/Pol II ChIP-Seq), as a proxy for transcription rate, and the ratio of EU-Seq over Pol II ChIP-Seq signal (EU-Seq/Pol II ChIP-Seq) upon RPC1 or RPAC1 depletion. Violin plots showing the quantification of the ratio changes for each group of gene sets in the right panel. The p value was calculated using the Mann–Whitney test. B Metaplots of H3K36me3 and S2P Pol II ChIP-Seq over the gene body regions of genebody-up mRNAs (N = 773, blue) and genebody-unaffected mRNAs (N = 3290, green) upon Pol III depletion. Violin plots showing the changes in ChIP-Seq signals over genebody-up or genebody-unaffected mRNA genes by Pol II upon depletion of Pol III, as shown in Fig. 3B (right). The p value was calculated using the Mann–Whitney test. C Genome browser track at the 8,269,424-8,592,237 region on chromosome 15 for Pol II ChIP-Seq signals in Pol III_degron and RPAC1_degron cells and SSRP1 ChIP-Seq signals in Pol III_degron cells that were untreated or treated with IAA for 1 h. PRO-Seq and ATAC-Seq in Pol III_degron cells that were untreated or treated with IAA for 1 h and Pol III ChIP-Seq in wild-type mESCs are shown in the same region. Only sense strand signals of PRO-Seq and ChAR-Seq are presented, and all tracks are flipped horizontally. D Upper panel: workflow of the DRB treatment assay with Pol III_degron cells that were untreated or treated with IAA for 1 h. Bottom panel: bar graphs showing relative ChIP enrichment normalized to input (5%) at the locus indicated in Fig. 7C. Each sample was analyzed with two technical replicates per biological replicate and two biological replicates in total. Statistical significance was evaluated by Student’s t test (**: <0.01, *: <0.05). E Heatmap representing the gene expression levels of the genebody-up genes upon Pol III depletion (n=773) from time-series RNA-Seq data (Pol III depletion for 0, 24, 48, and 96 h with two biological replicates). Each row represents the z score-transformed log2 (FPKM+1) values for one gene across different time points (green, low expression; red, high expression). F Working model for the cross-regulatory relationship between Pol II and Pol III by maintaining local chromatin structure. Pol II and Pol III help each other to destabilize nucleosome positioning and facilitate FACT-mediated chromatin structures maintenance when they occupy nearby regions in the genomeBack to article page