Characterization of KDIS genes.

A) Heat map displaying the measured poly(A) site reads for the wild-type (WT) and a <i>xrn1Δ</i> strain for KDIS and non KDIS genes. As expected, the bulk of the poly(A) site reads occur downstream of the stop codon, and a small fraction occurs prior to the start site (as expected from those originating from the upstream genes in tandem). KDIS genes do not display an increased number of poly(A) reads downstream of the start codon in the <i>xrn1Δ</i> strain. This suggests that XRN1 depletion does not lead to the accumulation of overlapping cryptic transcripts over the 5’region of KDIS. Plot generated from GSE40110 and GSE158548 using <i>DeepTools</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0308195#pone.0308195.ref035" target="_blank">35</a>]. Three individual replicates of WT and two of <i>xrn1Δ</i> strains are shown. B) Boxplots showing mRNA levels of KDIS vs. the rest of the genes (data from ref. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0308195#pone.0308195.ref020" target="_blank">20</a>]). The significance of the median comparisons was estimated using a Wilcoxon test: * = p< 0.05. C) Statistical study of KDIS genes. Venn diagrams show that KDIS genes do not significantly overlap those genes that depend more on Xrn1 for transcription activation and mRNA decay (<i>synthegradon</i>, Ref. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0308195#pone.0308195.ref018" target="_blank">18</a>]) and those genes whose mRNAs depend on Xrn1 for translation activation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0308195#pone.0308195.ref019" target="_blank">19</a>]. Statistical significance for every pair-wise comparison is indicated. (PDF)