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Fig. 7 | Genome Biology

Fig. 7

From: Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture

Fig. 7

Pol 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 genome

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