Xenbase Image ID: 154130

Fig. 4. c-Myc is a paused gene and CDK9 MO causes c-Myc to become more paused during development. (A) Histone methylation and RNA polymerase II (RNAPII) binding at the c-Myc gene. Profiles of H3K4me3 (marking active promoters and 5′ ends of gene bodies, green), H3K36me3 (showing active transcription, light green) and RNA Pol II (RNAPII, purple) (Hontelez et al., 2015) are visualised using the UCSC Genome Browser for the c-Myc gene on scaffold_6:7844903–7863621 (X. tropicalis genome assembly version 7.1). The transcriptional profile shows c-Myc to be a paused gene in Xenopus blastula and gastrula-stage embryos. RNA Pol II profile of the c-Myc gene at stage 16 from embryos injected with control MO or Cdk9s MO (blue). Note that the c-Myc gene is proportionately more paused in the cdk9 MO treated embryos. (B) RNA Pol II ChiP-seq on whole embryos injected with Control MO or Cdk9.S MO. i) Histogram plots showing the distribution of the Pausing Index values (RPKM TSS ±150 bp divided by the RPKM on the gene body) in log2 space for Control MO-injected (grey) and Cdk9.S MO-injected embryos (orange). The populations were shown to be significantly different from each other (Mann-Whitney P-value<2.2×10−16), indicative of RNAPII redistribution. ii) c-Myc is more highly paused in Cdk9 MO treated embryos. Scatter plots of RPKM on the gene body versus the transcriptional start site (tss) in Control MO (left panel) and Cdk9.S MO-injected embryos (right panel). The loss of Cdk9 causes an increase in the amount of RNA Pol II bound to the promoter compared to the rest of the gene body. The c-Myc gene is shown by the blue spot. Genes with the strongest increase in gene body RNAPII have the lowest increase in PI, suggesting that RNAPII stalls either at the promoter or in the gene body. The effects of RNAPII inhibition on transcript levels is shown in Fig. 3B. Image published in: Hatch VL et al. (2016) Copyright © 2016. Image reproduced with permission of the Publisher, Elsevier B. V. Larger Image Printer Friendly View

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