Eukaryotes share a conserved messenger RNA (mRNA) decay pathway in which bulk mRNA is degraded by exoribonucleases. In addition, it has become clear that more specialized mRNA decay pathways are initiated by endonucleolytic cleavage at particular sites. The transfer RNA (tRNA) splicing endonuclease (TSEN) has been studied for its ability to remove introns from pre-tRNAs. More recently it has been shown that single amino acid mutations in TSEN cause pontocerebellar hypoplasia. Other recent studies indicate that TSEN has other functions, but the nature of these functions has remained obscure. Here we show that yeast TSEN cleaves a specific subset of mRNAs that encode mitochondrial proteins, and that the cleavage sites are in part determined by their sequence. This provides an explanation for the counterintuitive mitochondrial localization of yeast TSEN. To identify these mRNA target sites, we developed a “comPARE” (comparative parallel analysis of RNA ends) bioinformatic approach that should be easily implemented and widely applicable to the study of endoribonucleases. The similarity of tRNA endonuclease-initiated decay to regulated IRE1-dependent decay of mRNA suggests that mRNA specificity by colocalization may be an important determinant for the degradation of localized mRNAs in a variety of eukaryotic cells.

真核生物共享一个保守的信使 RNA (mRNA) 衰变途径，其中大量 mRNA 被外切核糖核酸酶降解。此外，很明显，更特化的 mRNA 衰变途径是由特定位点的核酸内切酶切割引发的。已经研究了转移 RNA (tRNA) 剪接核酸内切酶 (TSEN) 从前体 tRNA 中去除内含子的能力。最近的研究表明，TSEN 中的单个氨基酸突变会导致桥脑小脑发育不全。最近的其他研究表明 TSEN 具有其他功能，但这些功能的性质仍然模糊不清。在这里，我们展示了酵母 TSEN 切割编码线粒体蛋白的特定 mRNA 子集，并且切割位点部分由它们的序列决定。这为酵母 TSEN 违反直觉的线粒体定位提供了解释。为了识别这些 mRNA 靶位点，我们开发了一种“comPARE”（RNA 末端的比较平行分析）生物信息学方法，该方法应该易于实施并广泛适用于核糖核酸内切酶的研究。tRNA 核酸内切酶引发的衰变与受调节的 IRE1 依赖的 mRNA 衰变的相似性表明，共定位的 mRNA 特异性可能是多种真核细胞中定位 mRNA 降解的重要决定因素。