Figure 2: Induced cut sites lead to downregulation of pre-existing transcription. | Nature Communications

Figure 2: Induced cut sites lead to downregulation of pre-existing transcription.

From: A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks

Figure 2

(a) Coverage profile plot representing the RPM of transcripts with AsiSI sites cut according to BLISS in induced (blue) and uninduced (red) samples for each genebody region: TES, transcription end site; TSS, transcription start site. Bold lines represent mean values, whereas semi-transparent shades around the mean curves represent the s.e.m. across the regions. (b) Coverage profile plot representing the RPM of transcripts with AsiSI sites uncut according to BLISS in induced (blue) and uninduced (red) samples for each genebody region. TES, transcription end site; TSS, transcription start site. (c) Distribution of the regularized-logarithm (rlog) fold change for genes with AsiSI sites cut according to BLISS and γH2AX ChIP-seq (blue) compared with the one of the rest of the genes (grey). Genes next to active AsiSI cut sites show significant shift towards downregulation (P<0.05, Wilcoxon test). (d) Distribution of the rlog fold change for genes with AsiSI sites uncut according to BLISS and γH2AX ChIP-seq (green) compared with the one of the rest of the genes (grey). Genes next to uncut AsiSI sites do not show significant shift towards downregulation (P=0.9996, Wilcoxon test). (e) qPCR validation of relative expression of eight randomly selected genes in induced (blue) versus uninduced (red) samples. Shown is the mean of biological replicates (n=3). Error bars show s.e.m. All reported differences where statistically significant (P<0.05; unpaired t test with Welch’s correction).

Back to article page