RNA Polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling

Abstract: In plants, the molecular function(s) of the nuclear localised 5’-3’ EXORIBONUCLEASES (XRNs) are unclear, however their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using Parallel Analysis of RNA Ends (PARE) we document a dramatic increase in uncapped RNA substrates of the XRNs in both sal1 and xrn2xrn3 mutants. We find that a major consequence of reducing SAL1 or XRN activity is RNA Polymerase II (Pol II) 3’ read-through. This occurs at 72% of expressed genes, demonstrating a major genome-wide role for the XRN-torpedo model of transcription termination in Arabidopsis. Read-through is speculated to have a negative effect on transcript abundance, however we do not observe this. Rather, we identify a strong association between read-though and increased transcript abundance of tandemly orientated downstream genes, strongly correlated with the proximity (<1,000bp) and expression of the upstream gene. We observe read-though in the proximity of 903 genes upregulated in the sal1-8 retrograde signaling mutant; thus, this phenomenon may directly account for up to 23% of genes upregulated in sal1-8. Using APX2 and AT5G43770 as exemplars, we genetically uncouple read-through loci from downstream genes to validate the principle of read-through mediated mRNA regulation, potentially providing one mechanism by which an obstensibly post-transcriptional exoribonuclease that targets uncapped RNAs could modulate gene expression. mRNA sequencing of pharmacologically treated Arabidopsis leaf tissue