Decoding Arabidopsis mRNA decay landscape shaped by XRN 5′-3′ exoribonucleases
Plant cells use a variety of exoribonucleases (XRNs) to remove mRNA processing remnants produced during mRNA maturation, or to clear damaged functional mRNA. Mining the substrates and products of XRNs can expand understanding of pre-mRNA processing and post-transcriptional regulation mechanism. By comparing the degradation fragments of Arabidopsis wild type and XRN mutants, we found that the nucleus-localized XRN3 is responsible for removing spliced introns and 3' fragments produced during pre-mRNA processing. In addition, the analysis of XRN3 substrate reveals that mRNA 3' -terminal cleavage often occurs after adenosine, which is contrast to the assumption of some previous studies. Through the comparison with the cytoplasmic exoribonuclease XRN4 mutant, we suggest that many degradation fragments highly accumulated in the wild type are products of XRN4 rather than its substrates. Further analysis of the XRN4 substrate revealed a novel endonucleolytic cleavage mechanism in the 3' untranslated regions. Our findings provide a revised view regarding mRNA processing and degradation, and also demonstrate the application of analyzing decay intermediates to uncover mRNA post-transcriptional regulation mechanism.