@article {672, title = {Surveillance of 3{\textquoteright} Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis.}, journal = {G3 (Bethesda)}, volume = {2}, year = {2012}, month = {2012 Apr}, pages = {487-98}, abstract = {Eukaryotes possess several RNA surveillance mechanisms that prevent undesirable aberrant RNAs from accumulating. Arabidopsis XRN2, XRN3, and XRN4 are three orthologs of the yeast 5{\textquoteright}-to-3{\textquoteright} exoribonuclease, Rat1/Xrn2, that function in multiple RNA decay pathways. XRN activity is maintained by FIERY1 (FRY1), which converts the XRN inhibitor, adenosine 3{\textquoteright}, 5{\textquoteright}-bisphosphate (PAP), into 5{\textquoteright}AMP. To identify the roles of XRNs and FRY1 in suppression of non-coding RNAs, strand-specific genome-wide tiling arrays and deep strand-specific RNA-Seq analyses were carried out in fry1 and xrn single and double mutants. In fry1-6, about 2000 new transcripts were identified that extended the 3{\textquoteright} end of specific mRNAs; many of these were also observed in genotypes that possess the xrn3-3 mutation, a partial loss-of-function allele. Mutations in XRN2 and XRN4 in combination with xrn3-3 revealed only a minor effect on 3{\textquoteright} extensions, indicating that these genes may be partially redundant with XRN3. We also observed the accumulation of 3{\textquoteright} remnants of many DCL1-processed microRNA (miRNA) precursors in fry1-6 and xrn3-3. These findings suggest that XRN3, in combination with FRY1, is required to prevent the accumulation of 3{\textquoteright} extensions that arise from thousands of mRNA and miRNA precursor transcripts.}, issn = {2160-1836}, doi = {10.1534/g3.111.001362}, author = {Kurihara, Yukio and Schmitz, Robert J and Nery, Joseph R and Schultz, Matthew D and Okubo-Kurihara, Emiko and Morosawa, Taeko and Tanaka, Maho and Toyoda, Tetsuro and Seki, Motoaki and Ecker, Joseph R} }