Skip to main content
Fig. 4 | Genome Biology

Fig. 4

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

Fig. 4

Pol III depletion affects the nucleosome occupancy of nearby mRNA genes. A Genebody-up mRNAs (blue), genebody-unaffected mRNAs (green), and unchanged mRNAs upon Pol III depletion (control, gray, unchanged genes) were defined by selecting the genes that were not at all affected by Pol III depletion; for details, see “Methods”) were clustered based on their distance from the nearest Pol III-bound peaks (upper) and expressed tRNAs (bottom) in 50 bp bins. B Sankey plot depicting relationships between Pol III and Pol II for the genebody-up genes and genebody-unaffected genes after Pol III depletion and four hypotheses in the subgroup, namely, transcription interference (interference), 3D interactions (looping), noncoding RNA (ncRNA), and nearby models. For detailed definitions, see Fig. S2E. C Working model for the cross-regulatory relationship between Pol III and Pol II by transcriptional interference, noncoding RNAs, 3D chromatin looping, and they occupy nearby but could not be explained the mechanisms listed above. D Volcano plots showing differentially accessible regions within active mRNA promoters (N=8845, ±1 kb centered on the TSS) identified by ATAC-seq upon depletion of Pol I, Pol II, and Pol III. The red dots represent a significant increase in chromatin accessibility, whereas the blue dots represent a significant decrease (adjusted P < 0.05). E ATAC-seq metaplots of mononucleosomes over the promoter regions of genebody-up mRNAs (N = 773, blue), genebody-unaffected mRNAs (N = 3290, green), and unchanged mRNAs (control, gray, for the definition, see “Methods”) upon Pol III depletion in Pol III_degron and Pol I_degron cells that were untreated or treated with IAA for 1 h (upper panel). Violin plots measuring the changes in promoter-proximal ATAC-seq mononucleosome signals over genebody-up or genebody-unaffected mRNA genes (bottom panel). Each violin plot shows the range of values, with the median indicated by a blue dot. The p value was calculated using the Mann–Whitney test. F Top panel: Composite metagene analysis of ATAC-Seq (upper) around the promoters, Pol II ChIP-Seq (middle), and PRO-Seq signals (bottom) around the gene bodies of mRNA genes in Pol III_degron cells with decreased and unchanged chromatin accessibility upon Pol III depletion, as shown in Fig. 4D. Promoters were defined as the regions within ± 2 kb of the transcription start site. For each metagene plot, the average profile (Y-axis) is displayed in normalized reads per million (RPM). Bottom panel: Violin plots (right) showing the quantification of ATAC-Seq, Pol II ChIP-Seq, and PRO-Seq signal changes for each group of gene sets shown in the top panel. The p value was calculated using the Mann–Whitney test

Back to article page