Skip to main content
Fig. 5 | Genome Biology

Fig. 5

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

Fig. 5

Local nucleosome positioning changes helps to explain the effects of Pol II on tRNA transcription. A Volcano plots showing the PRO-Seq signal changes over tRNA genes (N = 435) upon depletion of Pol I, Pol II, or Pol III. Statistically significant changes were determined from two biological replicates by the threshold criteria of an adjusted p value < 0.05 and absolute log2(fold change) >1 using DESeq2, with red representing upregulated genes and blue representing downregulated genes. B PRO-Seq in Pol II_degron cells under untreated conditions and after 1 h of IAA treatment. The Genome Browser track at the 21,166,370–21,202,236 region on chromosome 13 is shown with a bidirectional transcription signal. The y-axis shows the normalized read density in reads per kilobase per million mapped reads (RPKM). C The same data as described in Fig. 5B are shown for the 21,239,788–21,242,246 region on chromosome 13. D Under the same representations described in Fig. 4A, downregulated (N = 12, blue) and unchanged tRNA genes (N = 244, green) upon Pol II depletion in PRO-Seq were clustered based on their distance from the nearest expressed mRNAs and Pol II-bound peaks in 50-bp bins. E Under the same conditions described in Fig. 4D, differentially accessible sites around tRNA loci (N = 435, ±1 kb region centered on the tRNA genes) upon depletion of Pol I, Pol II, and Pol III are shown. F The ATAC-seq metaplots and violin plots shown are the same as those described in Fig. 4E but are based on the downregulated or unchanged tRNA genes upon Pol II depletion identified by PRO-Seq. The p value was calculated using the Mann–Whitney test

Back to article page