In plants, the molecular function(s) of the nucleus-localized 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, we documented a dramatic increase in uncapped RNA substrates of the XRNs in both sal1 and xrn2xrn3 mutants. We found that a major consequence of reducing SAL1 or XRN activity was RNA Polymerase II 3′ read-through. This occurred at 72% of expressed genes, demonstrating a major genome-wide role for the XRN-torpedo model of transcription termination in Arabidopsis (Arabidopsis thaliana). Read-through is speculated to have a negative effect on transcript abundance; however, we did not observe this. Rather, we identified a strong association between read-through and increased transcript abundance of tan-demly orientated downstream genes, strongly correlated with the proximity (less than 1,000 bp) and expression of the upstream gene. We observed read-through in the proximity of 903 genes up-regulated in the sal1-8 retrograde signaling mutant; thus, this phenomenon may account directly for up to 23% of genes up-regulated in sal1-8. Using APX2 and AT5G43770 as exemplars, we genetically uncoupled read-through loci from downstream genes to validate the principle of read-through-mediated mRNA regulation, providing one mechanism by which an ostensibly posttranscriptional exoribonuclease that targets uncapped RNAs could modulate gene expression.
Bibliographical noteFunding Information:
1We received financial assistance from the ARC Centre of Excellence in Plant Energy Biology (CE140100008). P.A.C., A.B.S., and D.R.G. were also supported by Grains Research and Development Council scholarships (GRS184, GRS11010, and GRS10683); S.R.E. by an ARC Discovery Early Career Researcher Award (DE150101206). D.R.G. and A.B.S. were also supported by Australian Research Training Program (RTP) scholarships. 2These authors contributed equally to the article. 3Author for contact: email@example.com. 4Senior author.
We received financial assistance from the ARC Centre of Excellence in Plant Energy Biology (CE140100008). P.A.C., A.B.S., and D.R.G. were also supported by Grains Research and Development Council scholarships (GRS184, GRS11010, and GRS10683); S.R.E. by an ARC Discovery Early Career Researcher Award (DE150101206). D.R.G. and A.B.S. were also supported by Australian Research Training Program (RTP) scholarships.We thank Milos Tanurdizc and Max Nekrasov for advice and assistance with optimizing Pol II ChIP assays and Su Yin Phua and Kai Chan for assistance with pharmacological treatments. We acknowledge the contributions of Terry Neeman toward the statistical analyses performed. We thank Nathan Springer for valuable discussions. We acknowledge the Biomolecular Resource Facility at the Australian National University and the Australian Genome Research Facility for performing Illumina sequencing. This investigation also was supported by the provision of plant growth facilities by the Australian Plant Phenomics Facility and computational infrastructure by the National Computational Infrastructure, both supported under the National Collaborative Research Infrastructure Strategy of the Australian Government.
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