XRN1-sensitive transcripts show specific transcript characteristics. Boxplots of (A) expression, (B) GC content, (C) translational efficiency, (D) 5′UTR length, (E) coding sequence (CDS) length, and (F) 3′UTR length of all transcripts within our data set. Grouped by their nature of change in expression and compared to the genome average as detected in our data set. Translational efficiency calculated as ribosome protected footprint FPKM/total RNA FPKM for each transcript. (G,H) MEME analysis of 3′UTR of 103 mRNAs reveal (G) 18 GU-rich sites across 10 unique transcripts and (H) 233 G-rich sites across 69 unique transcripts, motifs which may confer XRN1 sensitivity. (I) Similar analysis of 30 ncRNAs post-transcriptionally up-regulated in XRN1-depleted SAOS-2 cells reveals a similar G-rich motif to that observed in H (89 sites across 21 unique transcripts).
